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Genome-wide association studies (GWAS) in plants typically suffer from limited statistical power. An alternative to the logistical and cost challenge of increasing sample sizes is to gain power by meta-analysis using information from independent studies. We carried out GWAS for growth traits with six single-marker models and regional heritability mapping (RHM) in four Eucalyptus breeding populations independently and by Joint-GWAS, using gene and segment-based models, with data for 3373 individuals genotyped with a communal EUChip60KSNP platform. While single-single nucleotide polymorphism (SNP) GWAS hardly detected significant associations at high-stringency in each population, gene-based Joint-GWAS revealed nine genes significantly associated with tree height. Associations detected using single-SNP GWAS, RHM and Joint-GWAS set-based models explained on average 3-20% of the phenotypic variance. Whole-genome regression, conversely, captured 64-89% of the pedigree-based heritability in all populations. Several associations independently detected for the same SNPs in different populations provided unprecedented GWAS validation results in forest trees. Rare and common associations were discovered in eight genes involved in cell wall biosynthesis and lignification. With the increasing adoption of genomic prediction of complex phenotypes using shared SNPs and much larger tree breeding populations, Joint-GWAS approaches should provide increasing power to pinpoint discrete associations potentially useful toward tree breeding and molecular applications.
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Eucalyptus/genética , Genoma de Planta , Estudio de Asociación del Genoma Completo , Fitomejoramiento , Carácter Cuantitativo Heredable , Patrón de Herencia/genética , Desequilibrio de Ligamiento/genética , Polimorfismo de Nucleótido Simple/genética , Análisis de Componente PrincipalRESUMEN
BACKGROUND: The advent of high-throughput genotyping technologies coupled to genomic prediction methods established a new paradigm to integrate genomics and breeding. We carried out whole-genome prediction and contrasted it to a genome-wide association study (GWAS) for growth traits in breeding populations of Eucalyptus benthamii (n =505) and Eucalyptus pellita (n =732). Both species are of increasing commercial interest for the development of germplasm adapted to environmental stresses. RESULTS: Predictive ability reached 0.16 in E. benthamii and 0.44 in E. pellita for diameter growth. Predictive abilities using either Genomic BLUP or different Bayesian methods were similar, suggesting that growth adequately fits the infinitesimal model. Genomic prediction models using ~5000-10,000 SNPs provided predictive abilities equivalent to using all 13,787 and 19,506 SNPs genotyped in the E. benthamii and E. pellita populations, respectively. No difference was detected in predictive ability when different sets of SNPs were utilized, based on position (equidistantly genome-wide, inside genes, linkage disequilibrium pruned or on single chromosomes), as long as the total number of SNPs used was above ~5000. Predictive abilities obtained by removing relatedness between training and validation sets fell near zero for E. benthamii and were halved for E. pellita. These results corroborate the current view that relatedness is the main driver of genomic prediction, although some short-range historical linkage disequilibrium (LD) was likely captured for E. pellita. A GWAS identified only one significant association for volume growth in E. pellita, illustrating the fact that while genome-wide regression is able to account for large proportions of the heritability, very little or none of it is captured into significant associations using GWAS in breeding populations of the size evaluated in this study. CONCLUSIONS: This study provides further experimental data supporting positive prospects of using genome-wide data to capture large proportions of trait heritability and predict growth traits in trees with accuracies equal or better than those attainable by phenotypic selection. Additionally, our results document the superiority of the whole-genome regression approach in accounting for large proportions of the heritability of complex traits such as growth in contrast to the limited value of the local GWAS approach toward breeding applications in forest trees.
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Cruzamiento , Eucalyptus/crecimiento & desarrollo , Eucalyptus/genética , Estudio de Asociación del Genoma Completo , Genómica , Teorema de Bayes , Genoma de Planta/genética , Desequilibrio de Ligamiento , Fenotipo , Polimorfismo de Nucleótido SimpleRESUMEN
BACKGROUND: Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. RESULTS: Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. CONCLUSIONS: For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.
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Genómica , Técnicas de Genotipaje , Phaseolus/genética , Polimorfismo de Nucleótido Simple , Sitios Genéticos/genética , Genoma de Planta/genética , Desequilibrio de Ligamiento , Lluvia , TemperaturaRESUMEN
PURPOSE: This study determined the average distances and angles between anatomic landmarks within the orbit, with an emphasis on localization of the orbital process of the palatine bone. This information will help the surgeon with treatment planning and surgical procedures. PATIENTS AND METHODS: Four anatomic landmarks were identified retrospectively on computed tomograms of 100 adult Caucasian patients (50 men and 50 women): the top of the infraorbital margin superior to the infraorbital foramen (point A), the top of the orbital process of the palatine bone (point B), the anteriormost bony portion of the superior orbital fissure (point C), and the ventrolateral aspect of the bony entrance of the optic canal (point D). The distances between these points were measured, as were the angle between the medial wall of the orbit and a line connecting points A to D at the level of the optic nerve. RESULTS: The mean distances between the orbital rim (point A) and the orbital process of the palatine bone (point B) were 33.8 mm in men and 32.7 mm in women. Men had markedly larger bony orbits than women; however, women had a larger angle than men for the 2 orbits. CONCLUSION: Obtaining these measurements preoperatively can enable a safer and more predictable surgical approach to the orbit, which can help lower the risk of damaging important neighboring structures. A preformed reconstruction plate can be manufactured or a standard reconstruction plate can be customized according to these measurements; during reconstruction, they also can help adequately localize the posterior ledge, specifically the orbital process of the palatine bone. These 2 aspects could ensure a more precise reconstruction of the orbital floor.
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Puntos Anatómicos de Referencia , Órbita/anatomía & histología , Tomografía Computarizada por Rayos X , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Femenino , Humanos , Masculino , Persona de Mediana Edad , Órbita/diagnóstico por imagen , Órbita/cirugía , Valores de Referencia , Estudios Retrospectivos , Adulto JovenRESUMEN
Researchers have made great advances into the development and application of genomic approaches for common beans, creating opportunities to driving more real and applicable strategies for sustainable management of the genetic resource towards plant breeding. This work provides useful polymorphic single-nucleotide polymorphisms (SNPs) for high-throughput common bean genotyping developed by RAD (restriction site-associated DNA) sequencing. The RAD tags were generated from DNA pooled from 12 common bean genotypes, including breeding lines of different gene pools and market classes. The aligned sequences identified 23,748 putative RAD-SNPs, of which 3357 were adequate for genotyping; 1032 RAD-SNPs with the highest ADT (assay design tool) score are presented in this article. The RAD-SNPs were structurally annotated in different coding (47.00 %) and non-coding (53.00 %) sequence components of genes. A subset of 384 RAD-SNPs with broad genome distribution was used to genotype a diverse panel of 95 common bean germplasms and revealed a successful amplification rate of 96.6 %, showing 73 % of polymorphic SNPs within the Andean group and 83 % in the Mesoamerican group. A slightly increased He (0.161, n = 21) value was estimated for the Andean gene pool, compared to the Mesoamerican group (0.156, n = 74). For the linkage disequilibrium (LD) analysis, from a group of 580 SNPs (289 RAD-SNPs and 291 BARC-SNPs) genotyped for the same set of genotypes, 70.2 % were in LD, decreasing to 0.10 %in the Andean group and 0.77 % in the Mesoamerican group. Haplotype patterns spanning 310 Mb of the genome (60 %) were characterized in samples from different origins. However, the haplotype frameworks were under-represented for the Andean (7.85 %) and Mesoamerican (5.55 %) gene pools separately. In conclusion, RAD sequencing allowed the discovery of hundreds of useful SNPs for broad genetic analysis of common bean germplasm. From now, this approach provides an excellent panel of molecular tools for whole genome analysis, allowing integrating and better exploring the common bean breeding practices.
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ADN de Plantas/genética , Phaseolus/genética , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN/métodos , Análisis por Conglomerados , Evolución Molecular , Genotipo , Haplotipos , Alineación de SecuenciaRESUMEN
PURPOSE: The aim of this study was to find explanatory variables for objective and patient-reported long-term masticatory functioning in patients treated with maxillomandibular fixation for unilateral condylar neck or base fractures. These outcomes were compared to healthy control subjects. METHODS: Patients treated between 1996 and 2013 were enrolled in the study. Objective measurements included the mixing ability test (MAT) for masticatory performance, and range of motion of the mandible. Patient-reported measurements included the mandibular function impairment questionnaire (MFIQ) for masticatory ability, and the visual analogue scale for pain. Healthy subjects were recruited between October 2018 and January 2019, and performed the MAT and MFIQ. RESULTS: Twenty-one patients and 30 healthy subjects were included. The average follow-up period was 11.67 years. In adjusted regression analysis, the amount of occlusal units (OU) was associated with the MAT (P = 0.020; R2 = 0.253) and MFIQ (P = 0.001, R2 = 0.454). The MAT outcome was similar in both groups when correcting for OU (P = 0.001; R2 = 0.201). The MFIQ was inferior in the patient group (P = 0.001). CONCLUSION: Long-term masticatory performance was similar in patients with a history of condylar neck or base fracture and healthy subjects; however, masticatory ability was inferior in patients compared to healthy subjects.
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Fracturas Mandibulares , Humanos , Estudios Transversales , Fracturas Mandibulares/diagnóstico por imagen , Fracturas Mandibulares/cirugía , Fijación de Fractura , Cóndilo Mandibular/diagnóstico por imagen , Cóndilo Mandibular/cirugía , Mandíbula , Resultado del TratamientoRESUMEN
Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92% of the total assembly and 99% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.
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Evolución Molecular , Genética de Población , Genoma de Planta , Zea mays/genética , Alelos , Elementos Transponibles de ADN/genética , Sitios Genéticos , Haplotipos/genética , Anotación de Secuencia Molecular , Sistemas de Lectura Abierta/genética , Filogenia , Análisis de Secuencia de ADN , Zea mays/anatomía & histologíaRESUMEN
A biological life support system for spaceflight would capture carbon dioxide waste produced by living and working in space to generate useful organic compounds. Photosynthesis is the primary mechanism to fix carbon into organic molecules. Microalgae are highly efficient at converting light, water, and carbon dioxide into biomass, particularly under limiting, artificial light conditions that are a necessity in space photosynthetic production. Although there is great promise in developing algae for chemical or food production in space, most spaceflight algae growth studies have been conducted on solid agar-media to avoid handling liquids in microgravity. Here we report that breathable plastic tissue culture bags can support robust growth of Chlamydomonas reinhardtii in the Veggie plant growth chamber, which is used on the International Space Station (ISS) to grow terrestrial plants. Live cultures can be stored for at least 1 month in the bags at room temperature. The gene set required for growth in these photobioreactors was tested using a competitive growth assay with mutations induced by short-wave ultraviolet light (UVC) mutagenesis in either wild-type (CC-5082) or cw15 mutant (CC-1883) strains at the start of the assay. Genome sequencing identified UVC-induced mutations, which were enriched for transversions and non-synonymous mutations relative to natural variants among laboratory strains. Genes with mutations indicating positive selection were enriched for information processing genes related to DNA repair, RNA processing, translation, cytoskeletal motors, kinases, and ABC transporters. These data suggest that modification of DNA repair, signal transduction, and metabolite transport may be needed to improve growth rates in this spaceflight production system.
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Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans' yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r 2 sv ), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling â¼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed â¼220 genomic regions containing â¼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (â¼221 QTLs; 650 genes; r 2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.
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Forest tree breeding has been successful at delivering genetically improved material for multiple traits based on recurrent cycles of selection, mating, and testing. However, long breeding cycles, late flowering, variable juvenile-mature correlations, emerging pests and diseases, climate, and market changes, all pose formidable challenges. Genetic dissection approaches such as quantitative trait mapping and association genetics have been fruitless to effectively drive operational marker-assisted selection (MAS) in forest trees, largely because of the complex multifactorial inheritance of most, if not all traits of interest. The convergence of high-throughput genomics and quantitative genetics has established two new paradigms that are changing contemporary tree breeding dogmas. Genomic selection (GS) uses large number of genome-wide markers to predict complex phenotypes. It has the potential to accelerate breeding cycles, increase selection intensity and improve the accuracy of breeding values. Realized genomic relationships matrices, on the other hand, provide innovations in genetic parameters' estimation and breeding approaches by tracking the variation arising from random Mendelian segregation in pedigrees. In light of a recent flow of promising experimental results, here we briefly review the main concepts, analytical tools and remaining challenges that currently underlie the application of genomics data to tree breeding. With easy and cost-effective genotyping, we are now at the brink of extensive adoption of GS in tree breeding. Areas for future GS research include optimizing strategies for updating prediction models, adding validated functional genomics data to improve prediction accuracy, and integrating genomic and multi-environment data for forecasting the performance of genetic material in untested sites or under changing climate scenarios. The buildup of phenotypic and genome-wide data across large-scale breeding populations and advances in computational prediction of discrete genomic features should also provide opportunities to enhance the application of genomics to tree breeding.
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Many studies have been conducted to measure monaural azimuthal sound localization performance with different sounds varying in frequency and complexity, but few have used linguistic stimuli. The present experimental design used subjects' first names in a monaural azimuthal localization task. Analysis of response accuracy showed that subjects are not more accurate in localizing their own first name than in localizing other first names and that there was no significant advantage of one ear over another. Reaction times were shorter when the subjects localized their own first name than when they localized any other first names and there was no significant ear advantage, but localizing other first names took more time with the right than with the left ear. All stimuli were better and more quickly localized on the side of the open ear, and there was no difference in acuity or velocity of localization with the two different speaker voices used. These results suggest that first names are processed through the controlateral auditory pathway and can be analyzed in the right hemisphere.