212,067 research outputs found
USP tropical maize hybrid panel
No full text906 maize single-crosses obtained from a full dial- lel, according to Griffing’s method 4, divided into two heterotic groups, flint and dent, with 34 and 15 lines, respec- tively. Moreover, each heterotic group has a representative line, frequently used as the tester in our breeding program.
The experimental scheme used to evaluate the hybrids was an augmented block design (unreplicated trial) consisted of small blocks, each with 16 unique hybrids and two checks. Trials were carried out in Anhembi (22°50′51′′S, 48°01′06′′W, 466 m) and Piracicaba, at São Paulo State, Brazil (22°42′23′′S, 47°38′14′′W, 535 m), during the second growing season of 2016 and 2017, cultivated between January to June. In both sites and years, the hybrids were evaluated under two nitrogen (N) levels, low (LN) with 30 kg N ha−1, and normal (NN) with 100 kg N ha−1.
The genotyping of the 49 tropical inbred lines was per- formed by Affymetrix® platform, containing about 614,000 SNPs (Unterseer et al. 2014). Then, markers with low call rate (< 95%), minor allele frequency (MAF < 0.05) and heterozygous loci on at least one individual were removed. The missing markers were imputed using the snpReady R package. Finally, the resulting 146,365 SNPs high-quality polymorphic SNPs were used to build the artificial hybrids genomic matrix, deduced by combining the genotypes from its two parents
USP tropical maize hybrid panel
No full text906 maize single-crosses obtained from a full dial- lel, according to Griffing’s method 4, divided into two heterotic groups, flint and dent, with 34 and 15 lines, respec- tively. Moreover, each heterotic group has a representative line, frequently used as the tester in our breeding program.
The experimental scheme used to evaluate the hybrids was an augmented block design (unreplicated trial) consisted of small blocks, each with 16 unique hybrids and two checks. Trials were carried out in Anhembi (22°50′51′′S, 48°01′06′′W, 466 m) and Piracicaba, at São Paulo State, Brazil (22°42′23′′S, 47°38′14′′W, 535 m), during the second growing season of 2016 and 2017, cultivated between January to June. In both sites and years, the hybrids were evaluated under two nitrogen (N) levels, low (LN) with 30 kg N ha−1, and normal (NN) with 100 kg N ha−1.
The genotyping of the 49 tropical inbred lines was per- formed by Affymetrix® platform, containing about 614,000 SNPs (Unterseer et al. 2014). Then, markers with low call rate (< 95%), minor allele frequency (MAF < 0.05) and heterozygous loci on at least one individual were removed. The missing markers were imputed using the snpReady R package. Finally, the resulting 146,365 SNPs high-quality polymorphic SNPs were used to build the artificial hybrids genomic matrix, deduced by combining the genotypes from its two parents
Conférence de M. José R. Maia Neto
No full textMaia Neto José R. Conférence de M. José R. Maia Neto. In: École pratique des hautes études, Section des sciences religieuses. Annuaire. Tome 109, 2000-2001. 2000. pp. 429-431
Datasets of "Association mapping for image-based root traits in tropical maize under water stress in semi-arid regions"
No full textWater stress is the factor that most negatively impacts agricultural production. In this context, root system traits, such as length, surface area, volume, and mass, are paramount in water deficit studies, as they play a central role in plant growth, allocation, and acquisition of soil resources. However, the plant evaluation for them and under water stress is very difficult. Therefore, an alternative has been to obtain surrogate variables from image processing. Moreover, identifying genomic regions or genes associated with the expression of the root system under water deficit may allow breeding programs to outline more effective strategies for obtaining efficient genotypes. Hence, a public diversity panel composed of 360 inbred maize lines was evaluated via image-based root traits at phenological stage V6 (six expanded leaves) under well-water (WW) and water-stress (WS) conditions. Then, genetic association analyses (GWAS) were conducted for each image-based trait in WW and WS using the Fixed and Random Model Circulating Probability Unification (FarmCPU) method. A total of 23 markers were identified in association with all the traits in the two water supply conditions, 12 only in WW, four associated with traits in WW and WS, and seven exclusives to WS. All those genomic regions are associated with physiological mechanisms and molecular responses related to water deficit tolerance that can be explored in subsequent studies and by breeding programs to obtain more resilient genotypes for this condition. Furthermore, image-based features are a valuable tool to dissect root traits in WS conditions.'Here you can find all the data and scripts used to perform this study
TCGA: A TROPICAL CORN GERMPLASM ASSEMBLY FOR GENOMIC PREDICTION AND HIGH-THROUGHPUT PHENOTYPING STUDIES
No full textGenomic prediction (GS) studies using diversity panels are essential to identify genetic variations associated with traits of interest in maize. Unfortunately, most of these studies have been conducted on temperate germplasm and on a global germplasm collection in which tropical genotypes are under-represented. Nonetheless, a continuous effort has been directed to improving the accuracy of GS. While genotyping is currently a precise and efficient mechanized process, phenotyping is still laborious, low-throughput, and highly sensitive to environmental variations. Also, extreme shifts in the weather pattern due to climate change complicates the selection of superior genotypes with broad adaptability. In this context, adopting GS models that account for genotypes x environments reaction norms, crop growth models, and environmental covariates should increase the accuracy of genomic predictions. Thus, the objective of this project is to develop a diversity panel of tropical maize for genomic prediction studies that incorporate high-throughput phenotyping, plant growth models, and environmental covariables. For that, 360 tropical maize lines from ESALQ-USP, IAPAR, IAC, and CIMMYT will be genotyped and phenotyped using traditional methods and multispectral imaging in eight environments (two locations, two years, and two seasons). With this data, several GS models will be tested and compared for prediction accuracy and selection coincidence. Besides the development of novel GS models and high-throughput phenotyping protocols in tropical maize, we will also organize, characterize, and publicize a panel of tropical maize lines (data and genetic material) to the scientific community that will serve as the benchmark for new studies of this nature in tropical maize.
FAPESP (2017/24327-0
Genomic Dataset of the Commercial Germplasm in Brazil
No full textA few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Mon- santo® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commer- cial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent geno- mic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Syn- thetic), contributed to the development of the commercial Brazilian germplasms.
The hybrids (20) are in the rows and the markers (768) are in the columns. Quality control over data (MAF and Call Rate) was not performed. Genotypes are referred to by nitrogenous bases (eg G / G) and information lost by - / -
Tropical interspecific raspberry panel data
No full textMake available all datasets related to the "Tropical interspecific raspberry panel"https://bv.fapesp.br/pt/auxilios/106448/componentes-epidemiologicos-caracterizacao-de-danos-e-controle-de-ferrugens-tropicais-e-temperadas-e
Correction to: female reproductive organs of Brassica napus are more sensitive than male to transient heat stress
No full textThe article Female reproductive organs of Brassica napus are more sensitive than male to transient heat stress, written by Sheng Chen, Renu Saradadevi, Miriam S. Vidotti, Roberto Fritsche-Neto, Jose Crossa, Kadambot H. M. Siddique, Wallace A. Cowling, was originally published Online First without Open Access. After publication in volume 217: 117 the author decided to opt for Open Choice and to make the article an Open Access publication. Therefore, the copyright of the article has been changed t
Chronique des Papes, des Empereurs et des Évêques de Strasbourg, par Fritsche Closener.
No full textNumérisation effectuée à partir d'un document de substitution.Incipit (fol. 1 r°) : "Dis ist die kronica aller der bebeste, vnde aller der Romeschen Keiser die sit cristus geburte sint gewesen..." — Explicit (fol. 119 v°) : "Do man zalt M.CCCLXII. ior. Do kam ein Ertbidem zu Strasburg an den IX tage noch sant Peters dag... Des selben tages wart ouch dis buch vollebroht. von Fritsche Closener eime priester zu Strasburg." — Publié en dernier lieu par Hegel, die Chronieken der Deutschen Städte, VIII, 15-151 ; sur l'histoire du manuscrit, ibid., 11-13
Beta Regression in R
No full textThe class of beta regression models is commonly used by practitioners to model variables that assume values in the standard unit interval (0, 1). It is based on the assumption that the dependent variable is beta-distributed and that its mean is related to a set of regressors through a linear predictor with unknown coefficients and a link function. The model also includes a precision parameter which may be constant or depend on a (potentially different) set of regressors through a link function as well. This approach naturally incorporates features such as heteroskedasticity or skewness which are commonly observed in data taking values in the standard unit interval, such as rates or proportions. This paper describes the betareg package which provides the class of beta regressions in the R system for statistical computing. The underlying theory is briefly outlined, the implementation discussed and illustrated in various replication exercises.
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