scholarly journals The relevance of dominance and functional annotations to predict agronomic traits in hybrid maize

2019 ◽  
Author(s):  
Guillaume P. Ramstein ◽  
Sara J. Larsson ◽  
Jason P. Cook ◽  
Jode W. Edwards ◽  
Elhan S. Ersoz ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Agronomic Traits ◽  
Gene Annotation ◽  
The United States ◽  
Structural Features ◽  
Genetic Effects ◽  
Evolutionary Constraint ◽  
Maize Breeding ◽  
Heterotic Groups ◽  
Evolutionary Features

ABSTRACTHeterosis has been key to the development of maize breeding but describing its genetic basis has been challenging. Previous studies of heterosis have shown the contribution of within-locus complementation effects (dominance) and their differential importance across genomic regions. However, they have generally considered panels of limited genetic diversity and have shown little benefit to including dominance effects for predicting genotypic value in breeding populations. This study examined within-locus complementation and enrichment of genetic effects by functional classes in maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the United States (1,106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1,640 hybrids). We assayed three agronomic traits: days to silking (DTS), plant height (PH) and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results point to mechanisms by which heterosis arises through local complementation in proximal gene regions and suggest the relevance of dominance and gene annotations for genomic prediction in maize.

scholarly journals Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize

Genetics ◽  
2020 ◽  
Vol 215 (1) ◽  
pp. 215-230 ◽  
Author(s):  
Guillaume P. Ramstein ◽  
Sara J. Larsson ◽  
Jason P. Cook ◽  
Jode W. Edwards ◽  
Elhan S. Ersoz ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Agronomic Traits ◽  
Gene Annotation ◽  
Structural Features ◽  
Evolutionary Constraint ◽  
Diverse Populations ◽  
Heterotic Groups ◽  
Evolutionary Features ◽  
Functional Classes ◽  
Hybrid Maize

Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.

Formation of Heterotic Groups and Understanding Genetic Effects in a Provitamin A Biofortified Maize Breeding Program

Crop Science ◽  
2014 ◽  
Vol 54 (1) ◽  
pp. 14-24 ◽  
Author(s):  
Willy B. Suwarno ◽  
Kevin V. Pixley ◽  
Natalia Palacios-Rojas ◽  
Shawn M. Kaeppler ◽  
Raman Babu
Keyword(s):  
Genetic Effects ◽  
Breeding Program ◽  
Provitamin A ◽  
Maize Breeding ◽  
Heterotic Groups

Genetic Effects of 1BS Chromosome Arm on the Main Agronomic Traits in Chuanmai 42

2009 ◽  
Vol 35 (12) ◽  
pp. 2167-2173 ◽  
Author(s):  
Jun LI ◽  
Hui-Ting WEI ◽  
Su-Jie YANG ◽  
Chao-Su LI ◽  
Yong-Lu TANG ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Genetic Effects ◽  
Chromosome Arm

scholarly journals Descriptors of Cytochrome Inhibitors and Useful Machine Learning Based Methods for the Design of Safer Drugs

2021 ◽  
Vol 14 (5) ◽  
pp. 472
Author(s):  
Tyler C. Beck ◽  
Kyle R. Beck ◽  
Jordan Morningstar ◽  
Menny M. Benjamin ◽  
Russell A. Norris
Keyword(s):  
United States ◽  
Machine Learning ◽  
Drug Interactions ◽  
The United States ◽  
Structural Features ◽  
Physiochemical Properties ◽  
Drug Dosing ◽  
Therapeutic Outcomes ◽  
Cyp Inhibition ◽  
Cyp Inhibitors

Roughly 2.8% of annual hospitalizations are a result of adverse drug interactions in the United States, representing more than 245,000 hospitalizations. Drug–drug interactions commonly arise from major cytochrome P450 (CYP) inhibition. Various approaches are routinely employed in order to reduce the incidence of adverse interactions, such as altering drug dosing schemes and/or minimizing the number of drugs prescribed; however, often, a reduction in the number of medications cannot be achieved without impacting therapeutic outcomes. Nearly 80% of drugs fail in development due to pharmacokinetic issues, outlining the importance of examining cytochrome interactions during preclinical drug design. In this review, we examined the physiochemical and structural properties of small molecule inhibitors of CYPs 3A4, 2D6, 2C19, 2C9, and 1A2. Although CYP inhibitors tend to have distinct physiochemical properties and structural features, these descriptors alone are insufficient to predict major cytochrome inhibition probability and affinity. Machine learning based in silico approaches may be employed as a more robust and accurate way of predicting CYP inhibition. These various approaches are highlighted in the review.

scholarly journals Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Akio Onogi ◽  
Toshio Watanabe ◽  
Atsushi Ogino ◽  
Kazuhito Kurogi ◽  
Kenji Togashi
Keyword(s):  
Population Size ◽  
Genomic Prediction ◽  
Variance Components ◽  
Variance Component ◽  
Predictive Accuracy ◽  
Genetic Effect ◽  
Genetic Effects ◽  
Additive Effects ◽  
Additive Variance ◽  
Additive Genetic Effects

Abstract Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Results Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6–19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. Conclusions The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.

The biology of Canadian weeds. 108. Erucastrum gallicum (Willd.) O.E. Schulz

1998 ◽  
Vol 78 (1) ◽  
pp. 155-165 ◽  
Author(s):  
Suzanne I. Warwick ◽  
David A. Wall
Keyword(s):  
United States ◽  
Reproductive Output ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
The United States ◽  
Biological Information ◽  
Close Relative ◽  
Weed Biology ◽  
Germplasm Resource ◽  
Winter Annual

A review of biological information is provided for Erucastrum gallicum (Willd.) O.E. Schulz. A European native, it was introduced into Canada and the United States in the early 1900s and spread rapidly along the railroads. The species occurs in all the provinces and the Northwest Territories and is particularly abundant in the Prairie provinces and mid-western United States. It is a summer annual, rarely a winter annual or biennial species, and is characterized by high reproductive output. Plants occur most commonly on waste ground and along roadsides and railroads, followed by agricultural fields. Erucastrum gallicum is of allopolyploid origins (n = 15, 7 + 8 chromosomes), and contains a single multi-locus isozyme genotype. The species is a close relative of Brassica and is capable of limited genetic exchange with the canola species, B. rapa and B. napus. The possible transfer of genes from transgenic canola varieties to Erucastrum gallicum poses a remote, but potential, environmental risk. Populations of Erucastrum gallicum, including both Old World and North American populations, constitute a valuable germplasm resource as potential sources of beneficial agronomic traits, such as disease resistance for canola crop improvement. Key words: Dog mustard, Erucastrum gallicum, weed biology, risk assessment, germplasm, canola

scholarly journals Incorporating Gene Annotation into Genomic Prediction of Complex Phenotypes

Genetics ◽  
2017 ◽  
pp. genetics.300198.2017 ◽  
Author(s):  
Ning Gao ◽  
Johannes W. R. Martini ◽  
Zhe Zhang ◽  
Xiaolong Yuan ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Gene Annotation ◽  
Complex Phenotypes

scholarly journals Century-Long Dynamics of the Land Use Structure in the United States

2020 ◽  
pp. 220-231
Author(s):  
Valerij Minat
Keyword(s):  
United States ◽  
Land Use ◽  
Structural Changes ◽  
The United States ◽  
Structural Features ◽  
Summary Table ◽  
Land Use Structure ◽  
Periodic Dynamics ◽  
Space Dynamics ◽  
American Society

The paper studies the experience of American land use in the twentieth century on the territory of 48 contiguous continental states. Changes in time and space (dynamics) of the main indicators of distribution and use of land resources that form the structural appearance of the U.S. land fund are shown. Based on the analysis of the countrys land use structure, the resulting part of which is a summary table, the periodic dynamics of the land use structure (in twenty-year time intervals) is considered, and the dependence of structural changes in land use on the level and nature of the socio-economic development of American society is shown. The study of the age-old dynamics of structural features of American land use conducted on the basis of scientific materials of American scientists and data from official American statistics makes it possible to draw generalizing conclusions about the nature of land use in the United States, both in the whole country and in the regional aspect. As a result, the author has obtained a generalized scientific picture of how the structure of land use in the continental part of the country (without Alaska) has changed over the course of a century in the direction from maximum to optimal use of natural resources.

scholarly journals The Cytoplasm Origin Influence, the Teser Influence and the Nucleus-Cytoplasm Interactions Influence on Agronomic Traits for Maize Isonuclear Lines

2011 ◽  
Vol 68 (1) ◽  
Author(s):  
Camelia RACZ ◽  
Ioan HAS ◽  
Voichita HAS ◽  
Teodora ŞCHIOP ◽  
I COSTE
Keyword(s):  
Grain Yield ◽  
Dry Matter ◽  
Agronomic Traits ◽  
Vegetation Period ◽  
Negative Influence ◽  
Inbred Lines ◽  
Maize Breeding ◽  
High Productivity ◽  
Nucleus Transfer ◽  
Genetic Value

The maize is one of the most important crops in the world due to its high productivity and multiplexing usage in human nutrition, animal breeding and industry. The isonucleus inbred lines study has been initiated from the demand of clarifying if the cytoplasm source has a positive or negative influence on the corn cars, plants, grain traits and some maize cultural features. The research has been conducted in the experimental field provided by the Maize Breeding laboratory from ARDS Turda, ARDB Târgu-Mureş, ARDS Secuieni, ARDS Livada, ARDS Suceava in 2009. The cell nucleus transfer activity for 12 elite inbred lines on various cytoplasm types has begun in 1992 starting from the assumption that among cytoplasm of different origin could exist differences in the genetic value. The ultimate objective of breeding works is to obtain a higher grain yield and the yield quality to be at the desired level of farmers. For this reason it was studied the effect of different types of cytoplasm on grain yield, kernel dry matter at harvest and unbroken plants percentage at harvest, all these traits are important to achieve secure yield, mechanized harvestable. The kernel dry matter at harvest is one of the indicators of vegetation period, the most used in choice of early single crosses.

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