Analysis of historical selection in winter wheat

KEY MESSAGE: Modeling of the distribution of allele frequency over year of variety release identifies major loci involved in historical breeding of winter wheat. ABSTRACT: Winter wheat is a major crop with a rich selection history in the modern era of crop breeding. Genetic gains across economically important traits like yield have been well characterized and are the major force driving its production. Winter wheat is also an excellent model for analyzing historical genetic selection. As a proof of concept, we analyze two major collections of winter wheat varieties that were bred in Western Europe from 1916 to 2010, namely the Triticeae Genome (TG) and WAGTAIL panels, which include 333 and 403 varieties, respectively. We develop and apply a selection mapping approach, Regression of Alleles on Years (RALLY), in these panels, as well as in simulated populations. RALLY maps loci under sustained historical selection by using a simple logistic model to regress allele counts on years of variety release. To control for drift-induced allele frequency change, we develop a hybrid approach of genomic control and delta control. Within the TG panel, we identify 22 significant RALLY quantitative selection loci (QSLs) and estimate the local heritabilities for 12 traits across these QSLs. By correlating predicted marker effects with RALLY regression estimates, we show that alleles whose frequencies have increased over time are heavily biased toward conferring positive yield effect, but negative effects in flowering time, lodging, plant height and grain protein content. Altogether, our results (1) demonstrate the use of RALLY to identify selected genomic regions while controlling for drift, and (2) reveal key patterns in the historical selection in winter wheat and guide its future breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-022-04163-3

Analysis of historical selection in winter wheat

KEY MESSAGE: Modeling of the distribution of allele frequency over year of variety release identifies major loci involved in historical breeding of winter wheat. Winter wheat is a major crop with a rich selection history in the modern era of crop breeding. Genetic gains across economically important traits like yield have been well characterized and are the major force driving its production. Winter wheat is also an excellent model for analyzing historical genetic selection. As a proof of concept, we analyze two major collections of winter wheat varieties that were bred in Western Europe from 1916 to 2010, namely the Triticeae Genome (TG) and WAGTAIL panels, which include 333 and 403 varieties, respectively. We develop and apply a selection mapping approach, Regression of Alleles on Years (RALLY), in these panels, as well as in simulated populations. RALLY maps loci under sustained historical selection by using a simple logistic model to regress allele counts on years of variety release. To control for drift-induced allele frequency change, we develop a hybrid approach of genomic control and delta control. Within the TG panel, we identify 22 significant RALLY quantitative selection loci (QSLs) and estimate the local heritabilities for 12 traits across these QSLs. By correlating predicted marker effects with RALLY regression estimates, we show that alleles whose frequencies have increased over time are heavily biased toward conferring positive yield effect, but negative effects in flowering time, lodging, plant height and grain protein content. Altogether, our results (1) demonstrate the use of RALLY to identify selected genomic regions while controlling for drift, and (2) reveal key patterns in the historical selection in winter wheat and guide its future breeding

Origin Specific Genomic Selection: a simple process to optimize the favorable contribution of parents to progeny

Modern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favorable exotic alleles. Briefly, within a population derived from a bi-parental cross, we isolate alleles originating from the elite and exotic parents, which then allows us to separate out the predicted marker effects based on the allele origins. We validated the usefulness of OSGS using two nested association mapping (NAM) datasets: barley NAM (elite-exotic) and maize NAM (elite-elite), as well as by computer simulation. Our results suggest that OSGS works well in its goal to increase the contribution of favorable exotic alleles in bi-parental crosses, and it is possible to extend the approach to broader multi-parental populations

Nonlinear optical diode effect in a magnetic Weyl semimetal

Weyl semimetals have emerged as a promising quantum material system to discover novel electrical and optical phenomena, due to their combination of nontrivial quantum geometry and strong symmetry breaking. One crucial class of such novel transport phenomena is the diode effect, which is of great interest for both fundamental physics and modern technologies. In the electrical regime, giant electrical diode effect (the nonreciprocal transport) has been observed in Weyl systems. In the optical regime, novel optical diode effects have been theoretically considered but never probed experimentally. Here, we report the observation of the nonlinear optical diode effect (NODE) in the magnetic Weyl semimetal CeAlSi, where the magnetic state of CeAlSi introduces a pronounced directionality in the nonlinear optical second-harmonic generation (SHG). By physically reversing the beam path, we show that the measured SHG intensity can change by at least a factor of six between forward and backward propagation over a wide bandwidth exceeding 250 meV. Supported by density-functional theory calculations, we establish the linearly dispersive bands emerging from Weyl nodes as the origin of the extreme bandwidth. Intriguingly, the NODE directionality is directly controlled by the direction of magnetization. By utilizing the electronically conductive semimetallic nature of CeAlSi, we demonstrate current-induced magnetization switching and thus electrical control of the NODE in a mesoscopic spintronic device structure with current densities as small as 5 kA/cm$^2$. Our results advance ongoing research to identify novel nonlinear optical/transport phenomena in magnetic topological materials. The NODE also provides a way to measure the phase of nonlinear optical susceptibilities and further opens new pathways for the unidirectional manipulation of light such as electrically controlled optical isolators.Comment: 28 pages, 12 figure

Blood-Based Biomarkers of Aggressive Prostate Cancer

Purpose: Prostate cancer is a bimodal disease with aggressive and indolent forms. Current prostate-specific-antigen testing and digital rectal examination screening provide ambiguous results leading to both under-and over-treatment. Accurate, consistent diagnosis is crucial to risk-stratify patients and facilitate clinical decision making as to treatment versus active surveillance. Diagnosis is currently achieved by needle biopsy, a painful procedure. Thus, there is a clinical need for a minimally-invasive test to determine prostate cancer aggressiveness. A blood sample to predict Gleason score, which is known to reflect aggressiveness of the cancer, could serve as such a test. Materials and Methods: Blood mRNA was isolated from North American and Malaysian prostate cancer patients/controls. Microarray analysis was conducted utilizing the Affymetrix U133 plus 2·0 platform. Expression profiles from 255 patients/controls generated 85 candidate biomarkers. Following quantitative real-time PCR (qRT-PCR) analysis, ten disease-associated biomarkers remained for paired statistical analysis and normalization. Results: Microarray analysis was conducted to identify 85 genes differentially expressed between aggressive prostate cancer (Gleason score ≥8) and controls. Expression of these genes was qRT-PCR verified. Statistical analysis yielded a final seven-gene panel evaluated as six gene-ratio duplexes. This molecular signature predicted as aggressive (ie, Gleason score ≥8) 55% of G6 samples, 49% of G7(3+4), 79% of G7(4+3) and 83% of G8-10, while rejecting 98% of controls. Conclusion: In this study, we have developed a novel, blood-based biomarker panel which can be used as the basis of a simple blood test to identify men with aggressive prostate cancer and thereby reduce the overdiagnosis and overtreatment that currently results from diagnosis using PSA alone. We discuss possible clinical uses of the panel to identify men more likely to benefit from biopsy and immediate therapy versus those more suited to an “active surveillance” strategy

An Analysis and Research on the Transmission Ratio of Dye Sensitized Solar Cell Photoelectrodes by Using Different Etching Process

Classical photoelectrodes for Dye Sensitized Solar Cells (DSSCs) were fabricated by using the electrochemical method on the titanium (Ti) template, for that the fabrication process would influence the characteristics of the DSSCs. In this study, at first three different methods were used to etch Ti templates from 10 to 17 min, (1) polishing-chemical etching: Ti template was annealed at 450°C for 1 h, abraded using number 80 to 1500 SiC sheet, and then etched in a solution of 5% HF + 95% H2O; (2) electrochemical polishing-chemical etching: Ti template was annealed at 450°C for 1 h, electrolytic polishing with 42% CH3OH + 5% HClO4 + 53% HOCH2CH2OC4H9 solution, and the chemical-etching in a solution of 5% HF + 95% H2O; (3) chemical etching: Ti template was etched in a solution of 5% HF + 95% H2O and annealed at 450°C for 1 h. When the etching time was changed from 10 to 17 min, the thicknesses of Ti templates decreased from 75.3 μm to 14.8 μm, depending on the etching method. After etching process, the TiO2 nanotube arrays were fabricated as the photoelectrode of DSSCs by electrochemical process, in which the Ti as anode and platinum (Pt) as cathode. The electrolyte solution included C2H4(OH)2, NH4F, and deionized water. After annealing the grown TiO2 nanotube arrays at 450°C for 3 h, we would show that the etching process had large effect on the structure and transmittance ratio of the TiO2 nanotube arrays

Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, smalleffect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte

The Pan-STARRS1 Medium-deep Survey: Star Formation Quenching in Group and Cluster Environments

We make use of a catalog of 1600 Pan-STARRS1 groups produced by the probability friends-of-friends algorithm to explore how the galaxy properties, i.e., the specific star formation rate (SSFR) and quiescent fraction, depend on stellar mass and group-centric radius. The work is the extension of Lin et al. In this work, powered by a stacking technique plus a background subtraction for contamination removal, a finer correction and more precise results are obtained than in our previous work. We find that while the quiescent fraction increases with decreasing group-centric radius, the median SSFRs of star-forming galaxies in groups at fixed stellar mass drop slightly from the field toward the group center. This suggests that the main quenching process in groups is likely a fast mechanism. On the other hand, a reduction in SSFRs by ~0.2 dex is seen inside clusters as opposed to the field galaxies. If the reduction is attributed to the slow quenching effect, the slow quenching process acts dominantly in clusters. In addition, we also examine the density–color relation, where the density is defined by using a sixth-nearest-neighbor approach. Comparing the quiescent fractions contributed from the density and radial effect, we find that the density effect dominates the massive group or cluster galaxies, and the radial effect becomes more effective in less massive galaxies. The results support mergers and/or starvation as the main quenching mechanisms in the group environment, while harassment and/or starvation dominate in clusters