Select and Sequence of a Segregating Sugar Beet Population Provides Genomic Perspective of Host Resistance to Seedling Rhizoctonia solani Infection

Understanding the genetic basis of polygenic traits is a major challenge in agricultural species, especially in non-model systems. Select and sequence (SnS) experiments carried out within existing breeding programs provide a means to simultaneously identify the genomic background of a trait while improving the mean phenotype for a population. Using pooled whole genome sequencing (WGS) of selected and unselected bulks derived from a synthetic outcrossing sugar beet population EL57 (PI 663212), which segregates for seedling rhizoctonia resistance, we identified a putative genomic background involved in conditioning a resistance phenotype. Population genomic parameters were estimated to measure fixation (He), genome divergence (FST), and allele frequency changes between bulks (DeltaAF). We report on the genome wide patterns of variation resulting from selection and highlight specific genomic features associated with resistance. Expected heterozygosity (He) showed an increased level of fixation in the resistant bulk, indicating a greater selection pressure was applied. In total, 1,311 biallelic loci were detected as significant FST outliers (p < 0.01) in comparisons between the resistant and susceptible bulks. These loci were detected in 206 regions along the chromosomes and contained 275 genes. We estimated changes in allele frequency between bulks resulting from selection for resistance by leveraging the allele frequencies of an unselected bulk. DeltaAF was a more stringent test of selection and recovered 186 significant loci, representing 32 genes, all of which were also detected using FST. Estimates of population genetic parameters and statistical significance were visualized with respect to the EL10.2 physical map and produced a candidate gene list that was enriched for function in cell wall metabolism and plant disease resistance, including pathogen perception, signal transduction, and pathogen response. Specific variation associated with these genes was also reported and represents genetic markers for validation and prediction of resistance to Rhizoctonia. Select and sequence experiments offer a means to characterize the genetic base of sugar beet, inform selection within breeding programs, and prioritize candidate variation for functional studies.

A Conterminous USA-Scale Map of Relative Tidal Marsh Elevation

Tidal wetlands provide myriad ecosystem services across local to global scales. With their uncertain vulnerability or resilience to rising sea levels, there is a need for mapping flooding drivers and vulnerability proxies for these ecosystems at a national scale. However, tidal wetlands in the conterminous USA are diverse with differing elevation gradients, and tidal amplitudes, making broad geographic comparisons difficult. To address this, a national-scale map of relative tidal elevation (Z*MHW), a physical metric that normalizes elevation to tidal amplitude at mean high water (MHW), was constructed for the first time at 30 × 30-m resolution spanning the conterminous USA. Contrary to two study hypotheses, watershed-level median Z*MHW and its variability generally increased from north to south as a function of tidal amplitude and relative sea-level rise. These trends were also observed in a reanalysis of ground elevation data from the Pacific Coast by Janousek et al. (Estuaries and Coasts 42 (1): 85–98, 2019). Supporting a third hypothesis, propagated uncertainty in Z*MHW increased from north to south as light detection and ranging (LiDAR) errors had an outsized effect under narrowing tidal amplitudes. The drivers of Z*MHW and its variability are difficult to determine because several potential causal variables are correlated with latitude, but future studies could investigate highest astronomical tide and diurnal high tide inequality as drivers of median Z*MHW and Z*MHW variability, respectively. Watersheds of the Gulf Coast often had propagated Z*MHW uncertainty greater than the tidal amplitude itself emphasizing the diminished practicality of applying Z*MHW as a flooding proxy to microtidal wetlands. Future studies could focus on validating and improving these physical map products and using them for synoptic modeling of tidal wetland carbon dynamics and sea-level rise vulnerability analyses.

Reintroducing the GeoNames that features the land and water near the Montufar and Bingay Points in Prieto Diaz, Sorsogon, Philippines

Purpose–The paper aims to generate analytical data to reintroduce the geographic naming based on the existing coastwise feature names as part of contextualizing the ecosystem relative to risk reality phenomena that are based on the actual land and water uses inthe study area.Method–ArcGIS platform was used to assess the following: (i) coastwise feature names based on the Special Report of the United States Board of Geographic Names Relating to the Geographic Names in the Philippine Island, (ii) Topographical features and feature names, (iii) politico-administrativeand planning subdivisions, (iv) income classification of the study area, (v) natural and physical map features of the study area, (vi) disaster risk reality phenomenon, (vii) The Agta IPs environmental and Disaster RiskReduction Practices relative to the ecosystem and actual uses of land and water in the study areaResults–Coastwise feature naming describes the physical environment that features the mountain, river, historical, cultural, or events being named, etc. The Coastwise feature names are essential in improving and promoting eco-tourism activities on the coast of Prieto Diaz as the home of the indigenous people who traditionally settle and move to another settlement merely remaining speaking their mother tongue"Agta Tabangnon and Bicol Sorsogon''. Although the income classification of Prieto Diaz is low, during the COVID-19 lockdown the locally produced food supply was sufficient to feed Prieto Diaznon. This implies that the coping capacity during pandemic somehow hinted that the land and water utilization remain stable municipal wide. It generally implies the friendliness of Prieto Diaznon which resembles the indigenous people's friendliness to the environment before the Spaniards colonization. The natural resources are generally conserved and protected although some built-up areas were impacted by the calamities and natural hazards. But in terms of disaster risk reality was calculated to be 92% which means the study area is somewhat resilient to resilient municipalities. The remaining 8% are areas mostly located in low-lying and coastal areas.Conclusion–The coastwise feature names relating to the geographic names in the Philippine Islands remain in use for coastal directions, research to monitor sedimentation significant in assessing the general development of a regional understanding of the vegetation and climate dynamics, and weather forecasts. This study concludes that the coastwise feature names or geographic names are significant to characterize the riskor resiliency realities of the old barrios up to the present barangays. Furthermore, the coastwise feature names relating to the geographic names in the Philippine Islands remain useful to attract more tourists and researchers to visit a place virtually or on-site during and after the COVID-19 pandemic.Recommendations–Reintroduction of the geographic names by way of contextualization risk or resilience reality theory of Abante (2021a;2020a) and incorporating the of the Popper (1978)theory on "worldof contents of thought",Meiring (1993) theory on 'place names', and Quine (1953) cited the Strawson's logical theory of reference on backing the naming with descriptions can also reintroduce a place starting from the 'VisitangDaan' myth up to the present barangays via internet especially during the new normal after COVID-19 pandemic to strengthen linkages and trading.

The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophila melanogaster Line with the Rif11; SuURES Su(var)3-906 Mutations Suppressing Underreplication

Although heterochromatin makes up 40% of the Drosophila melanogaster genome, its organization remains little explored, especially in polytene chromosomes, as it is virtually not represented in them due to underreplication. Two all-new approaches were used in this work: (i) with the use of a newly synthesized Drosophila line that carries three mutations, Rif11, SuURESand Su(var)3-906, suppressing the underreplication of heterochromatic regions, we obtained their fullest representation in polytene chromosomes and described their structure; (ii) 20 DNA fragments with known positions on the physical map as well as molecular genetic features of the genome (gene density, histone marks, heterochromatin proteins, origin recognition complex proteins, replication timing sites and satellite DNAs) were mapped in the newly polytenized heterochromatin using FISH and bioinformatics data. The borders of the heterochromatic regions and variations in their positions on arm 3L have been determined for the first time. The newly polytenized heterochromatic material exhibits two main types of morphology: a banding pattern (locations of genes and short satellites) and reticular chromatin (locations of large blocks of satellite DNA). The locations of the banding and reticular polytene heterochromatin was determined on the physical map.

Design, preparation, and characterization of auxetic weft backed weave fabrics based on Miura origami structure

The metamaterials with negative Poisson’s ratio are called auxetic materials, which as a branch of metamaterials has drawn a lot of attention in many areas. Existing auxetic knitting textiles combine flexibility and auxeticity, however the loose structure has been a main disadvantage for its application. In this study, we fabricated Miura origami structure fabrics by weaving technology in order to acquire more stable auxetic textiles. The results show that using the combination of fabric structure type and elastic yarns, an origami structure can be realized in a jacquard loom. In the Miura origami structure, the crease pattern can be separated into three parts, unfolding areas, convex areas, and concave areas. One warp system and two weft systems are compounded together, in which a weft backed weave is used to get elastic floats in the convex and concave areas, and to make the fabrics bend to the concave side. The physical map showed that the fabrics had a clear Miura origami structure and the unfolding areas were flat and even. On the basis of the designed geometric pattern, weft backed weaves can be used to construct different folded areas, spandex wrapped PET (Polyester) and inelastic PET are selected as two weft systems for weaving. Meanwhile, the Miura origami fabrics exhibit distinct in-plane negative Poisson’s ratio and out-of-plane positive Poisson’s ratio. Apart from the Miura origami structure, other origami and paper-cut structures can be realized using this method, and these special auxetic textiles have potential in protective cloths, ornamented textiles, wearable devices, and flexible sensors.

Meta-Analysis Reveals Consensus Genomic Regions Associated with Multiple Disease Resistance in Wheat ( Triticum Aestivum L.)

In wheat, meta-QTLs (MQTLs), and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103; fusarium head blight (FHB), 184; karnal bunt (KB), 66, and loose smut (LS), 14. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of initial QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed genes (DEGs). Among the DEGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping of MDR genes and marker-assisted breeding.

Construction of Consensus Genetic Map With Applications in Gene Mapping of Wheat (Triticum aestivum L.) Using 90K SNP Array

Wheat is one of the most important cereal crops worldwide. A consensus map combines genetic information from multiple populations, providing an effective alternative to improve the genome coverage and marker density. In this study, we constructed a consensus map from three populations of recombinant inbred lines (RILs) of wheat using a 90K single nucleotide polymorphism (SNP) array. Phenotypic data on plant height (PH), spike length (SL), and thousand-kernel weight (TKW) was collected in six, four, and four environments in the three populations, and then used for quantitative trait locus (QTL) mapping. The mapping results obtained using the constructed consensus map were compared with previous results obtained using individual maps and previous studies on other populations. A simulation experiment was also conducted to assess the performance of QTL mapping with the consensus map. The constructed consensus map from the three populations spanned 4558.55 cM in length, with 25,667 SNPs, having high collinearity with physical map and individual maps. Based on the consensus map, 21, 27, and 19 stable QTLs were identified for PH, SL, and TKW, much more than those detected with individual maps. Four PH QTLs and six SL QTLs were likely to be novel. A putative gene called TraesCS4D02G076400 encoding gibberellin-regulated protein was identified to be the candidate gene for one major PH QTL located on 4DS, which may enrich genetic resources in wheat semi-dwarfing breeding. The simulation results indicated that the length of the confidence interval and standard errors of the QTLs detected using the consensus map were much smaller than those detected using individual maps. The consensus map constructed in this study provides the underlying genetic information for systematic mapping, comparison, and clustering of QTL, and gene discovery in wheat genetic study. The QTLs detected in this study had stable effects across environments and can be used to improve the wide adaptation of wheat cultivars through marker-assisted breeding.

Experimental Study on the Relationship between Compression Stability and Deformation Localization of Viscous/Brittle Rock-Like Materials

Rock-like materials often exhibit irregular failure deformation under long-term service conditions, and the deformation and failure of asphalt and concrete materials is a serious problem that leads to subgrade failure. In this study, two different viscous/brittle rock-like materials were prepared by the in situ loading and optical speckle synchronous monitoring test method, and the evolution characteristics of the deformation field were studied during compression. The formation process of the compression deformation localization of rock-like materials and their relationship with stability were analyzed. A quantitative description of the compression deformation stage and localization characteristics of the viscous/brittle rock-like materials is presented. The results can be summarized as follows. At the initial stage of compression, the deformation localization zone of viscous/brittle rock-like materials begins to expand from the middle area to the surrounding area. Preliminary results of the deformation localization of the linear elastic deformation stage were obtained. The failure cloud image is completely formed at the peak, which is consistent with the failure physical map. The deformation process of compression can be quantitatively described using the deformation localization characteristics of rock-like materials.

Haplotype Reconstruction in Connected Tetraploid F1 Populations

In diploid species, many multiparental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. In these populations, haplotype reconstruction has been used as a standard practice to increase the power of QTL detection in comparison with the marker-based association analysis. However, such software tools for polyploid species are few and limited to a single biparental F1 population. In this paper, a statistical framework for haplotype reconstruction has been developed and implemented in the software PolyOrigin for connected tetraploid F1 populations with shared parents, regardless of the number of parents or mating design. Given a genetic or physical map of markers, PolyOrigin first phases parental genotypes, then refines the input marker map, and finally reconstructs offspring haplotypes. PolyOrigin can utilize single nucleotide polymorphism (SNP) data coming from arrays or from sequence-based genotyping; in the latter case, bi-allelic read counts can be used (and are preferred) as input data to minimize the influence of genotype calling errors at low depth. With extensive simulation we show that PolyOrigin is robust to the errors in the input genotypic data and marker map. It works well for various population designs with ≥ offspring per parent and for sequences with read depth as low as 10x. PolyOrigin was further evaluated using an autotetraploid potato dataset with a 3 × 3 half-diallel mating design. In conclusion, PolyOrigin opens up exciting new possibilities for haplotype analysis in tetraploid breeding populations.