Mapping Agronomic and Quality Traits in Elite Durum Wheat Lines under Differing Water Regimes

Final grain production and quality in durum wheat are affected by biotic and abiotic stresses. The association mapping (AM) approach is useful for dissecting the genetic control of quantitative traits, with the aim of increasing final wheat production under stress conditions. In this study, we used AM analyses to detect quantitative trait loci (QTL) underlying agronomic and quality traits in a collection of 294 elite durum wheat lines from CIMMYT (International Maize and Wheat Improvement Center), grown under different water regimes over four growing seasons. Thirty-seven significant marker-trait associations (MTAs) were detected for sedimentation volume (SV) and thousand kernel weight (TKW), located on chromosomes 1B and 2A, respectively. The QTL loci found were then confirmed with several AM analyses, which revealed 12 sedimentation index (SDS) MTAs and two additional loci for SV (4A) and yellow rust (1B). A candidate gene analysis of the identified genomic regions detected a cluster of 25 genes encoding blue copper proteins in chromosome 1B, with homoeologs in the two durum wheat subgenomes, and an ubiquinone biosynthesis O-methyltransferase gene. On chromosome 2A, several genes related to photosynthetic processes and metabolic pathways were found in proximity to the markers associated with TKW. These results are of potential use for subsequent application in marker-assisted durum wheat-breeding programs

Lack of influence of the environment in the earliest stages of massive galaxy formation

We investigate how the environment affects the assembly history of massive galaxies. For that purpose, we make use of SHARDS and HST spectro-photometric data, whose depth, spectral resolution, and wavelength coverage allow to perform a detailed analysis of the stellar emission as well as obtaining unprecedentedly accurate photometric redshifts. This expedites a sufficiently accurate estimate of the local environment and a robust derivation of the star formation histories of a complete sample of 332 massive galaxies ($\mathrm{>10^{10}M_{\odot}}$) at redshift $1\leq z \leq 1.5$ in the GOODS-N field. We find that massive galaxies in this redshift range avoid the lowest density environments. Moreover, we observed that the oldest galaxies in our sample with with mass-weighted formation redshift $\mathrm{\overline{z}_{M-w} \geq 2.5}$, avoid the highest density regions, preferring intermediate environments. Younger galaxies, including those with active star formation, tend to live in denser environments ($\Sigma = \mathrm{5.0_{1.1}^{24.8}\times 10^{10}M_{\odot}Mpc^{-2}}$). This behavior could be expected if those massive galaxies starting their formation first would merge with neighbors and sweep their environment earlier. On the other hand, galaxies formed more recently ($\overline{z}_{M-w} < 2.5$) are accreted into large scale structures at later times and we are observing them before sweeping their environment or, alternatively, they are less likely to affect their environment. However, given that both number and mass surface densities of neighbor galaxies is relatively low for the oldest galaxies, our results reveal a very weak correlation between environment and the first formation stages of the earliest massive galaxies.Comment: Accepted for publication in MNRA

Genetic dissection of agronomic and quality traits based on association mapping and genomic selection approaches in durum wheat grown in Southern Spain

Climatic conditions affect the growth, development and final crop production. As wheat is of paramount importance as a staple crop in the human diet, there is a growing need to study its abiotic stress adaptation through the performance of key breeding traits. New and complementary approaches, such as genome-wide association studies (GWAS) and genomic selection (GS), are used for the dissection of different agronomic traits. The present study focused on the dissection of agronomic and quality traits of interest (initial agronomic score, yield, gluten index, sedimentation index, specific weight, whole grain protein and yellow colour) assessed in a panel of 179 durum wheat lines (Triticum durum Desf.), grown under rainfed conditions in different Mediterranean environments in Southern Spain (Andalusia). The findings show a total of 37 marker-trait associations (MTAs) which affect phenotype expression for three quality traits (specific weight, gluten and sedimentation indexes). MTAs could be mapped on the A and B durum wheat subgenomes (on chromosomes 1A, 1B, 2A, 2B and 3A) through the recently available bread wheat reference assembly (IWGSC RefSeqv1). Two of the MTAs found for quality traits (gluten index and SDS) corresponded to the known Glu-B1 and Glu-A1 loci, for which candidate genes corresponding to high molecular weight glutenin subunits could be located. The GS prediction ability values obtained from the breeding materials analyzed showed promising results for traits as grain protein content, sedimentation and gluten indexes, which can be used in plant breeding programs.Junta de Andalucía (Andalusian Regional Government) P12- AGR-0482FEDER P12- AGR-0482MINECO (Spanish Ministry of Economy, Industry and Competitiveness) AGL2016-77149-C2-1-

Interdisciplinary Tutoring for the Development of Professional-Simulation Role-Plays

Current society is characterised by a growing tendency of interrelationship among different professional sectors in order to offer their potential customers a better quality of certain products or process. Thereby, and in the context of this interdisciplinarity, higher-education teachers must frame their teaching methodologies mainly focused on the acquisition of certain competences so that students could guarantee the development of their professional abilities. Taking this as a premise, we have performed an interdisciplinary role-play so as to allow our students to acquire those professional competences. However, to carry out this performance a well-organised tutorial plan, divided into several tutoring sessions, was required to succeed in the use of this active methodology

Probing the Star Formation Main Sequence down to 10810^{8} M⊙_\odot at 1.0<z<3.01.0<z<3.0

We investigate the star formation main sequence (MS) (SFR-M$_{\star}$) down to 10$^{8-9}\mathrm{M}_\odot$ using a sample of 34,061 newly-discovered ultra-faint ($27\lesssim i \lesssim 30$ mag) galaxies at $1<z<3$ detected in the GOODS-N field. Virtually these galaxies are not contained in previous public catalogs, effectively doubling the number of known sources in the field. The sample was constructed by stacking the optical broad-band observations taken by the HST/GOODS-CANDELS surveys as well as the 25 ultra-deep medium-band images gathered by the GTC/SHARDS project. Our sources are faint (average observed magnitudes $\sim28.2$ mag, $\sim27.9$ mag), blue (UV-slope $\sim-1.9$), star-forming (rest-frame colors $\sim0.10$ mag, $\sim0.17$ mag) galaxies. These observational characteristics are identified with young (mass-weighted age $\sim0.014$ Gyr) stellar populations subject to low attenuations ($\sim0.30$ mag). Our sample allows us to probe the MS down to $10^{8.0}\,\mathrm{M}_\odot$ at $z=1$ and $10^{8.5}\,\mathrm{M}_\odot$ at $z=3$, around 0.6 dex deeper than previous analysis. In the low-mass galaxy regime, we find an average value for the slope of 0.97 at $1<z<2$ and 1.12 at $2<z<3$. Nearly $\sim$60% of our sample presents stellar masses in the range $10^{6-8}$ M$_\odot$ between $1<z<3$. If the slope of the MS remained constant in this regime, the sources populating the low-mass tail of our sample would qualify as starburst galaxies.Comment: 34 pages, 16 figures, 9 tables. Accepted for publication to Ap

An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases

Clinical exome (CE) sequencing has become a first-tier diagnostic test for hereditary diseases; however, its diagnostic rate is around 30–50%. In this study, we aimed to increase the diagnostic yield of CE using a custom reanalysis algorithm. Sequencing data were available for three cohorts using two commercial protocols applied as part of the diagnostic process. Using these cohorts, we compared the performance of general and clinically relevant variant calling and the efficacy of an in-house bioinformatic protocol (FJD-pipeline) in detecting causal variants as compared to commercial protocols. On the whole, the FJD-pipeline detected 99.74% of the causal variants identified by the commercial protocol in previously solved cases. In the unsolved cases, FJD-pipeline detects more INDELs and non-exonic variants, and is able to increase the diagnostic yield in 2.5% and 3.2% in the re-analysis of 78 cancer and 62 cardiovascular cases. These results were considered to design a reanalysis, filtering and prioritization algorithm that was tested by reassessing 68 inconclusive cases of monoallelic autosomal recessive retinal dystrophies increasing the diagnosis by 4.4%. In conclusion, a guided NGS reanalysis of unsolved cases increases the diagnostic yield in genetic disorders, making it a useful diagnostic tool in medical geneticsWe want to thank the participants for consenting to the use of their data for the study. We would like to thank all technical staff in the genetics service of the Fundación Jiménez Díaz University Hospital for conducting the sequencing and segregation analysis. We also thank Oliver Shaw (IIS-FJD) for editorial assistance. This work was supported by the Instituto de Salud Carlos III (ISCIII) of the Spanish Ministry of Health (FIS; PI16/00425, PI19/00321, PI18/00579 and PI20/00851), Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER, 06/07/0036), IIS-FJD BioBank (PT13/0010/0012), Comunidad de Madrid (CAM, RAREGenomics Project, B2017/BMD-3721), Ramón Areces Foundation (4019/012), Conchita Rábago Foundation, and the University Chair UAM-IIS-FJD of Genomic Medicine. R.R. is supported by a postdoctoral fellowship of the Comunidad de Madrid (2019-T2/BMD-13714), L.d.l.F. is supported by the platform technician contract of ISCIII (CA18/00017), IPR is supported by a PhD studentship from the predoctoral program from ISCIII (FI17/ 00192), I.F.I. is supported by a grant from the Comunidad de Madrid (CAM, PEJ-2017- AI/BMD7256), G.N.M. is supported by a grant from the Comunidad de Madrid (PEJ2020-AI/BMD-18610), A.D. is supported by a PhD studentship from the predoctoral program from ISCIII (FI18/00123), B.A. is supported by a Juan Rodes program from ISCIII (JR17/00020), C.R. is supported by a PhD studentship from the Conchita Rabago Foundation and PM and MC are supported by a Miguel Servet program contract from ISCIII (CP16/00116 and CPII17/00006, respectively). The funders played no role in study design, data collection, data analysis, manuscript preparation, and/or publication decision

Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications

ESRETNET Study Group, The ERDC Study Group, The Associated Clinical Study Group.Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.This work was supported by the Instituto de Salud Carlos III (ISCIII) of the Spanish Ministry of Health (FIS; PI16/00425 and PI19/00321), Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER, 06/07/0036), IIS-FJD BioBank (PT13/0010/0012), Comunidad de Madrid (CAM, RAREGenomics Project, B2017/BMD-3721), European Regional Development Fund (FEDER), the Organización Nacional de Ciegos Españoles (ONCE), Fundación Ramón Areces, Fundación Conchita Rábago and the University Chair UAM-IIS-FJD of Genomic Medicine. Irene Perea-Romero is supported by a PhD fellowship from the predoctoral Program from ISCIII (FI17/00192). Ionut F. Iancu is supported by a grant from the Comunidad de Madrid (CAM, PEJ-2017-AI/BMD7256). Marta del Pozo-Valero is supported by a PhD grant from the Fundación Conchita Rábago. Berta Almoguera is supported by a Juan Rodes program from ISCIII (JR17/00020). Pablo Minguez is supported by a Miguel Servet program from ISCIII (CP16/00116). Marta Corton is supported by a Miguel Servet program from ISCIII (CPII17/00006)

Probing the earliest phases in the formation of massive galaxies with simulated HST+JWST imaging data from Illustris

We use the Illustris-1 simulation to explore the capabilities of the $\textit{Hubble}$ and $\textit{James Webb Space Telescope}$ data to analyze the stellar populations in high-redshift galaxies, taking advantage of the combined depth, spatial resolution, and wavelength coverage. For that purpose, we use simulated broad-band ACS, WFC3 and NIRCam data and 2-dimensional stellar population synthesis (2D-SPS) to derive the integrated star formation history (SFH) of massive (M$_{\ast}>10^{10}\,$M$_{\odot}$) simulated galaxies at $110^{11}\,$M$_{\odot}$ galaxy. In particular, we explore the potential of HST and JWST datasets reaching a depth similar to those of the CANDELS and ongoing CEERS observations, respectively, and concentrate on determining the capabilities of this dataset for characterizing the first episodes in the SFH of local M$_{\ast}>10^{11}\,$M$_{\odot}$ galaxies by studying their progenitors at $z>1$. The 2D-SPS method presented in this paper has been calibrated to robustly recover the cosmic times when the first star formation episodes occurred in massive galaxies, i.e., the first stages in their integrated SFHs. In particular, we discuss the times when the first 1% to 50% of their total stellar mass formed in the simulation. We demonstrate that we can recover these ages with typical median systematic offset of less than 5% and scatter around 20%-30%. According to our measurements on Illustris data, we are able to recover that local M$_{\ast}>10^{11}\,$M$_{\odot}$ galaxies would have started their formation by $z=16$, forming the first 5% of their stellar mass present at $z \sim 1$ by $z=4.5$, 10% by $z=3.7$, and 25% by $z=2.7$.Comment: 28 pages, 13 figures, 4 tables. ApJ in press. Summary of changes from original submission: the major change is that we now include in Sec. 6 the comparison of the results obtained for our sample of massive 1 < z < 4 progenitors with those obtained by considering all massive galaxies at 1 < z < 4 in the simulated images. Several figures and sections have been update

Life beyond 30: Probing the −20 < M UV < −17 Luminosity Function at 8 < z < 13 with the NIRCam Parallel Field of the MIRI Deep Survey

We present the ultraviolet luminosity function and an estimate of the cosmic star formation rate density at 8 8 galaxy candidates based on their dropout nature in the F115W and/or F150W filters, a high probability for their photometric redshifts, estimated with three different codes, being at z > 8, good fits based on χ2 calculations, and predominant solutions compared to z < 8 alternatives. We find mild evolution in the luminosity function from z ∼ 13 to z ∼ 8, i.e., only a small increase in the average number density of ∼0.2 dex, while the faint-end slope and absolute magnitude of the knee remain approximately constant, with values α = − 2.2 ± 0.1, and M* = − 20.8 ± 0.2 mag. Comparing our results with the predictions of state-of-the-art galaxy evolution models, we find two main results: (1) a slower increase with time in the cosmic star formation rate density compared to a steeper rise predicted by models; (2) nearly a factor of 10 higher star formation activity concentrated in scales around 2 kpc in galaxies with stellar masses ∼108M⊙ during the first 350 Myr of the universe, z ∼ 12, with models matching better the luminosity density observational estimations ∼150 Myr later, by z ∼ 9