Elite Panel Research Articles

Genetic gains in IRRI’s rice salinity breeding and elite panel development as a future breeding resource

Key messageEstimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains.Genetic gain is a crucial parameter to check the breeding program's success and help optimize future breeding strategies for enhanced genetic gains. To estimate the genetic gains in IRRI’s salinity breeding program and identify the best genotypes based on high breeding values for grain yield (kg/ha), we analyzed the historical data from the trials conducted in the IRRI, Philippines and Bangladesh. A two-stage mixed-model approach accounting for experimental design factors and a relationship matrix was fitted to obtain the breeding values for grain yield and estimate genetic trends. A positive genetic trend of 0.1% per annum with a yield advantage of 1.52 kg/ha was observed in IRRI, Philippines. In Bangladesh, we observed a genetic gain of 0.31% per annum with a yield advantage of 14.02 kg/ha. In the released varieties, we observed a genetic gain of 0.12% per annum with a 2.2 kg/ha/year yield advantage in the IRRI, Philippines. For the Bangladesh dataset, a genetic gain of 0.14% per annum with a yield advantage of 5.9 kg/ha/year was observed in the released varieties. Based on breeding values for grain yield, a core set of the top 145 genotypes with higher breeding values of > 2400 kg/ha in the IRRI, Philippines, and > 3500 kg/ha in Bangladesh with a reliability of > 0.4 were selected to develop the elite breeding panel. Conclusively, a recurrent selection breeding strategy integrated with novel technologies like genomic selection and speed breeding is highly required to achieve higher genetic gains in IRRI’s salinity breeding programs.

Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines

Estimating genetic trends using historical data is an important parameter to check the success of the breeding programs. The estimated genetic trends can act as a guideline to target the appropriate breeding strategies and optimize the breeding program for improved genetic gains. In this study, 17 years of historical data from IRRI’s rice drought breeding program was used to estimate the genetic trends and assess the breeding program's success. We also identified top-performing lines based on grain yield breeding values as an elite panel for implementing future population improvement-based breeding schemes. A two-stage approach of pedigree-based mixed model analysis was used to analyze the data and extract the breeding values and estimate the genetic trends for grain yield under non-stress, drought, and in combined data of non-stress and drought. Lower grain yield values were observed in all the drought trials. Heritability for grain yield estimates ranged between 0.20 and 0.94 under the drought trials and 0.43–0.83 under non-stress trials. Under non-stress conditions, the genetic gain of 0.21% (10.22 kg/ha/year) for genotypes and 0.17% (7.90 kg/ha/year) for checks was observed. The genetic trend under drought conditions exhibited a positive trend with the genetic gain of 0.13% (2.29 kg/ha/year) for genotypes and 0.55% (9.52 kg/ha/year) for checks. For combined analysis showed a genetic gain of 0.27% (8.32 kg/ha/year) for genotypes and 0.60% (13.69 kg/ha/year) for checks was observed. For elite panel selection, 200 promising lines were selected based on higher breeding values for grain yield and prediction accuracy of > 0.40. The breeding values of the 200 genotypes formulating the core panel ranged between 2366.17 and 4622.59 (kg/ha). A positive genetic rate was observed under all the three conditions; however, the rate of increase was lower than the required rate of 1.5% genetic gain. We propose a recurrent selection breeding strategy within the elite population with the integration of modern tools and technologies to boost the genetic gains in IRRI’s drought breeding program. The elite breeding panel identified in this study forms an easily available and highly enriched genetic resource for future recurrent selection programs to boost the genetic gains.

Designing grant-review panels for better funding decisions: Lessons from an empirically calibrated simulation model

ObjectivesTo explore how factors relating to grades and grading affect the correctness of choices that grant-review panels make among submitted proposals. To identify interventions in panel design that may be expected to increase the correctness of choices. MethodExperimentation with an empirically-calibrated computer simulation model of panel review. Model parameters are set in accordance with procedures at a national science funding agency. Correctness of choices among research proposals is operationalized as agreement with the choices of an elite panel. ConclusionsThe simulation model generates several hypotheses to guide further research. Increasing the number of grades used by panel members increases the correctness of simulated choices among submitted proposals. Collective decision procedures giving panels a greater capacity for discriminating among proposals also increase correctness. Surprisingly, differences in grading standards among panel members do not appreciably decrease correctness.

Editorial Note and Statistical Analysis for Women's Health: Open Access

Journal of Women’s Health, Issues and Care: Open Access (ISSN: 2325-9795), expresses gratitude to all its elite panel of editorial board members for their continuous efforts, support and encouragement throughout the publication journey of the journal and congratulates them for making this journal to achieve its goals and becoming successful as one of the leading and well-recognized presenter of scientific outcomes in the field of women health.

Editorial Note for Translational Medicine

Journal “Translational Medicine” expresses sincere gratitude to all its elite panel of editorial board members for their continuous efforts, valuable support and encouragement throughout the publication journey of the journal, and the journal publish quality of research and becoming as one of the leading and well-recognized broadcaster of scientific outcomes in the field of studies related to findings developments from public health, global health policy planning and implementation research.

Discovery of interesting new polymorphisms in a sugar beet (elite times exotic) progeny by comparison with an elite panel

Key messageThe comparison of QTL detection performed on an elite panel and an (elite times exotic) progeny shows that introducing exotic germplasm into breeding programs can bring new interesting allelic diversity.Selection of stable varieties producing the highest amount of extractable sugar per hectare (ha), resistant to diseases, and respecting environmental criteria is undoubtedly the main target for sugar beet breeding. As sodium, potassium, and alpha-amino nitrogen in sugar beets are the impurities that have the biggest negative impact on white sugar extraction, it is interesting to reduce their concentration in further varieties. However, domestication history and strong selection pressures have affected the genetic diversity needed to achieve this goal. In this study, quantitative trait locus (QTL) detection was performed on two populations, an (elite times exotic) sugar beet progeny and an elite panel, to find potentially new interesting regions brought by the exotic accession. The three traits linked with impurities content were studied. Some QTLs were detected in both populations, the majority in the elite panel because of most statistical power. Some of the QTLs were colocated and had favorable effect in the progeny since the exotic allele was linked with a decrease in the impurity content. A few number of favorable QTLs were detected in the progeny, only. Consequently, introgressing exotic genetic material into sugar beet breeding programs can allow the incorporation of new interesting alleles.

Performance evaluation of gastrointestinal viral ELIte panel multiplex RT-PCR assay for the diagnosis of rotavirus, adenovirus and astrovirus infection

Rotavirus, adenovirus, norovirus and astrovirus are considered to be among the major causes of sporadic cases and outbreaks of acute gastroenteritis globally. Rapid and accurate identification of enteric viruses is still a challenge for the clinical laboratory. Recently, several molecular platforms for the detection of viral enteric pathogens have become available. In this study, the diagnostic accuracy of InGenius Gastrointestinal Viral (GV) Elite Panel, a newly developed one-step multiplex real-time RT-PCR assay simultaneously detecting rotavirus, adenovirus and astrovirus, was evaluated retrospectively analyzing an archival collection of 128 stool samples of children hospitalized with acute gastroenteritis. The overall sensitivity and specificity for the GV assay was 100% and 96.2% for rotavirus, 96.9% and 100% for astrovirus, 100% and 100% for adenovirus, respectively. The InGenius GV assay showed a high concordance with the reference methods and was able to detect all tested genotypes of rotavirus (including G1, G3, G4, G9 and G12P[8] and G2P[4]), adenovirus and astrovirus (AstV-1 and 2). Studies of considerable sample size are required to determine robust Cycle threshold cut-off values to effectively correlate infection to disease. These preliminary results suggest that InGenius GV assay can be recommended as a valuable method for accurate diagnosis of epidemic and sporadic gastroenteritis.

Identifying an Elite Panel of Apple Rootstock Germplasm with Contrasting Root Resistance to Pythium ultimum

Apple replants disease (ARD), incited by a soil borne pathogen complex, is a major obstacle to establishing an economically viable apple orchard at replant sites. The predominant control method is pre-plant chemical fumigation of orchard soil, which is expensive and comes with environmental and regulatory concerns. To maximize the exploitation of host resistance for ARD management, high quality resistance phenotypes in apple roots to ARD pathogen infection are required for elucidating the underlying resistance mechanisms. In this study, root resistance responses to Pythium ultimum infection were systematically evaluated among the ‘Ottawa 3’ × ‘Robusta 5’ (O3R5) F1 progeny. Tissue culture-based micro propagation was employed to generate genetically-defined and age-equivalent apple plants for repeated infection assays. A wide range of plant survival rates were observed, with fewer than 30% for the susceptible genotypes and over 80% for the resistant ones. The levels of root and shoot biomass reduction among the surviving plants varied substantially between the most resistant genotypes and the most susceptible genotypes. Contrasting necrosis patterns were demonstrated along the infected roots between resistant and susceptible genotypes using a novel glass-box pot for continuous microscopic observation. Swift necrosis occurred across the entire root system within 24 hours for the susceptible genotypes; in sharp contrast, evidently deterred root necrosis was observed for the resistant genotypes. A well-defined boundary separating healthy and necrotic root tissues were often accompanied with the infected roots of resistant genotypes, while the profuse growth of P. ultimum hyphae was specifically associated with the infected roots of susceptible genotypes. The results from this study represented the first comprehensive and detailed effort undertaken to define the genotype-specific resistance responses in apple roots as they are challenged by a soil-borne pathogen.

Identification of genomic regions for grain yield and yield stability and their epistatic interactions

The task of identifying genomic regions conferring yield stability is challenging in any crop and requires large experimental data sets in conjunction with complex analytical approaches. We report findings of a first attempt to identify genomic regions with stable expression and their individual epistatic interactions for grain yield and yield stability in a large elite panel of wheat under multiple environments via a genome wide association mapping (GWAM) approach. Seven hundred and twenty lines were genotyped using genotyping-by-sequencing technology and phenotyped for grain yield and phenological traits. High gene diversity (0.250) and a moderate genetic structure (five groups) in the panel provided an excellent base for GWAM. The mixed linear model and multi-locus mixed model analyses identified key genomic regions on chromosomes 2B, 3A, 4A, 5B, 7A and 7B. Further, significant epistatic interactions were observed among loci with and without main effects that contributed to additional variation of up to 10%. Simple stepwise regression provided the most significant main effect and epistatic markers resulting in up to 20% variation for yield stability and up to 17% gain in yield with the best allelic combination.

EVALUATION AGILITY INDEXES AND ASPECTS OF HUMAN FORCE

New approaches arrival in production, management, and industrial reengineering influence soft factors more than hard factors in present era. In this agile era, it is not more possible to plan and predict everything beforehand. Therefore, using traditional methods won’t be useful anymore. Agile human force should have collection of flexible abilities to cope with instabilities. In this research, first a model is provided using related studies to agility then a model based on elites ideas was prepared and formulated by Delphi method and judgmental and chain sampling and the confirmed four-step Delphi model of elite panel by five-aspect and various indexes of agility abilities of human force are finalized as following: intelligence and awareness, multiple competences, knowledge management, enabling culture, and information system. Equipping human force to these abilities will have organizations not only reduce risk of facing with uncertainties, but also take step in agility path. Dynamisms and making chain of abilities for human resources is a strategy that can be open many deadlines in developing path.

Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.).

BackgroundGray Leaf Spot (GLS causal agents Cercospora zeae-maydis and Cercospora zeina) is one of the most important foliar diseases of maize in all areas where the crop is being cultivated. Although in the USA the situation with GLS severity is not as critical as in sub-Saharan Africa or Brazil, the evidence of climate change, increasing corn monoculture as well as the narrow genetic base of North American resistant germplasm can turn the disease into a serious threat to US corn production. The development of GLS resistant cultivars is one way to control the disease. In this study we combined the high QTL detection power of genetic linkage mapping with the high resolution power of genome-wide association study (GWAS) to precisely dissect QTL controlling GLS resistance and identify closely linked molecular markers for robust marker-assisted selection and trait introgression.ResultsUsing genetic linkage analysis with a small bi-parental mapping population, we identified four GLS resistance QTL on chromosomes 1, 6, 7, and 8, which were validated by GWAS. GWAS enabled us to dramatically increase the resolution within the confidence intervals of the above-mentioned QTL. Particularly, GWAS revealed that QTLGLSchr8, detected by genetic linkage mapping as a locus with major effect, was likely represented by two QTL with smaller effects. Conducted in parallel, GWAS of days-to-silking demonstrated the co-localization of flowering time QTL with GLS resistance QTL on chromosome 7 indicating that either QTLGLSchr7 is a flowering time QTL or it is a GLS resistance QTL that co-segregates with the latter. As a result, this genetic linkage – GWAS hybrid mapping system enabled us to identify one novel GLS resistance QTL (QTLGLSchr8a) and confirm with more refined positions four more previously mapped QTL (QTLGLSchr1, QTLGLSchr6, QTLGLSchr7, and QTLGLSchr8b). Through the novel Single Donor vs. Elite Panel method we were able to identify within QTL confidence intervals SNP markers that would be suitable for marker-assisted selection of gray leaf spot resistant genotypes containing the above-mentioned GLS resistance QTL.ConclusionThe application of a genetic linkage – GWAS hybrid mapping system enabled us to dramatically increase the resolution within the confidence interval of GLS resistance QTL by-passing labor- and time-intensive fine mapping. This method appears to have a great potential to accelerate the pace of QTL mapping projects. It is universal and can be used in the QTL mapping projects in any crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2171-3) contains supplementary material, which is available to authorized users.

Breeding patterns and cultivated beets origins by genetic diversity and linkage disequilibrium analyses.

Genetic diversity in worldwide population of beets is strongly affected by the domestication history, and the comparison of linkage disequilibrium in worldwide and elite populations highlights strong selection pressure. Genetic relationships and linkage disequilibrium (LD) were evaluated in a set of 2035 worldwide beet accessions and in another of 1338 elite sugar beet lines, using 320 and 769 single nucleotide polymorphisms, respectively. The structures of the populations were analyzed using four different approaches. Within the worldwide population, three of the methods gave a very coherent picture of the population structure. Fodder beet and sugar beet accessions were grouped together, separated from garden beets and sea beets, reflecting well the origins of beet domestication. The structure of the elite panel, however, was less stable between clustering methods, which was probably because of the high level of genetic mixing in breeding programs. For the linkage disequilibrium analysis, the usual measure (r (2)) was used, and compared with others that correct for population structure and relatedness (r S (2) , r V (2) , r VS (2)). The LD as measured by r (2) persisted beyond 10 cM within the elite panel and fell below 0.1 after less than 2 cM in the worldwide population, for almost all chromosomes. With correction for relatedness, LD decreased under 0.1 by 1 cM for almost all chromosomes in both populations, except for chromosomes 3 and 9 within the elite panel. In these regions, the larger extent of LD could be explained by strong selection pressure.

Artificial Intelligence researchers confront sci-fi scenarios

Everything from smartphone viruses to machines that self-replicate are being debated by an elite panel of AI scientists, as they debate what's possible and what's not