scholarly journals Accounting for spatial trends in multi-environment diallel analysis in maize breeding

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258473
Author(s):  
Igor Ferreira Coelho ◽  
Marco Antônio Peixoto ◽  
Tiago de Souza Marçal ◽  
Arthur Bernardeli ◽  
Rodrigo Silva Alves ◽  
...  
Keyword(s):  
Block Design ◽  
Standard Procedure ◽  
Diallel Analysis ◽  
Genetic Evaluation ◽  
Information Criteria ◽  
Joint Analysis ◽  
Ratio Test ◽  
Maize Breeding ◽  
Spatial Trends ◽  
Spa Model

Spatial trends represent an obstacle to genetic evaluation in maize breeding. Spatial analyses can correct spatial trends, which allow for an increase in selective accuracy. The objective of this study was to compare the spatial (SPA) and non-spatial (NSPA) models in diallel multi-environment trial analyses in maize breeding. The trials consisted of 78 inter-populational maize hybrids, tested in four environments (E1, E2, E3, and E4), with three replications, under a randomized complete block design. The SPA models accounted for autocorrelation among rows and columns by the inclusion of first-order autoregressive matrices (AR1 ⊗ AR1). Then, the rows and columns factors were included in the fixed and random parts of the model. Based on the Bayesian information criteria, the SPA models were used to analyze trials E3 and E4, while the NSPA model was used for analyzing trials E1 and E2. In the joint analysis, the compound symmetry structure for the genotypic effects presented the best fit. The likelihood ratio test showed that some effects changed regarding significance when the SPA and NSPA models were used. In addition, the heritability, selective accuracy, and selection gain were higher when the SPA models were used. This indicates the power of the SPA model in dealing with spatial trends. The SPA model exhibits higher reliability values and is recommended to be incorporated in the standard procedure of genetic evaluation in maize breeding. The analyses bring the parents 2, 10 and 12, as potential parents in this microregion.

scholarly journals Combining Ability and Heterosis in Diallel Analysis of Maize (Zea mays L.) Lines

2020 ◽  
Vol 9 (1) ◽  
pp. 188-200
Author(s):  
Francis Chukwuma Onejeme ◽  
Emmanuel Ogbonna Okporie ◽  
Chinedu Emmanuel Eze
Keyword(s):  
Grain Yield ◽  
Combining Ability ◽  
Block Design ◽  
Diallel Analysis ◽  
Diallel Cross ◽  
Maize Breeding ◽  
Ear Height ◽  
Check Variety ◽  
Additive Genetic Effects ◽  
Positive Heterosis

A sound breeding program for maize improvement is very important to meet the demands of the growing population. Therefore, combining ability and heterosis were studied in a 4 x 4 full diallel cross in maize for growth attributes, yield and its contributing traits. Randomized Complete Block Design (RCBD) with four replicates was used to study the general combining ability of parents, specific combining ability of F1s (including reciprocals) and heterosis of the F1s over commercial check variety on selected agronomic characters. Genotype was highly significant for all the traits studied. The combining abilities (GCA and SCA) and reciprocal mean squares were highly significant for most studied characters. The ratio of GCA/SCA was not less than unity for studied traits excepted for days to anthesis and ear height. The results indicated that the additive genetic effects were more important and played major role in studied traits. Thus, results revealed GCA effects for the parental lines (PL). Where ‘PL2’ was excellent combiner for number of tassels and cob circumference and ‘PL3’ was good combiner for days to silking and grain yield (t.h-1). While ‘PL4’ for short height. Majority of the F1s from the GCA effects showed high SCA effects. This F1 (PL2 x PL3) performed best amongst. However, several reciprocals were not desirable. Heterosis estimation was carried out using a commercial check, Oba super II. When commercial check was used, the percent heterosis especially on grain yield varied from -8.89 to 22.62%. Among the twelve F1s, nine of the crosses exhibited significant positive heterosis for grain yield (t.h-1). Those F1s that showed significant positive and/or negative desirable traits for SCA effects and significant positive heterosis could be used for varietal development in maize breeding. And conservation of those parents that exhibited high GCA effects be considered as well.

scholarly journals Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 393-399 ◽  
Author(s):  
Spencer V Muse ◽  
Brandon S Gaut
Keyword(s):  
Nucleotide Substitution ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Joint Analysis ◽  
Ratio Test ◽  
Substitution Rates ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates ◽  
Nucleotide Substitution Rates ◽  
Evolutionary Lineages

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.

scholarly journals Diallel analysis of maize resistance to Phaeosphaeria maydis

2004 ◽  
Vol 61 (1) ◽  
pp. 36-42 ◽  
Author(s):  
Herberte Pereira da Silva ◽  
José Roberto Moro
Keyword(s):  
Disease Severity ◽  
Block Design ◽  
Genetic Resistance ◽  
Diallel Analysis ◽  
Inbred Lines ◽  
Randomized Block Design ◽  
Whole Plant ◽  
Sources Of Variation ◽  
Specific Hybrid ◽  
Additive Genetic Effects

In breeding programs directed towards genetic resistance against diseases, the estimation of genetic parameters that control resistance allows the introduction of resistance into suscetible germplasm to be clearly focused. The purposes of this study were to estimate heterosis effects, and the general (GCA) and specific (SCA) combining abilities by using two rating methods for resistance to Phaeosphaeria maydis in a diallel analysis of 36 F1 maize hybrids and their nine inbred lines. Trials were conducted in three environments. Disease severity was evaluated in the whole plant (PI) and in the leaf positioned just below the point of insertion of the main ear (AFA). The trials followed a randomized block design with plots represented by a 5 m long rows. Differences among combining ability estimates for different environments and in both evaluation methods showed significant effects (P < 0.01) for environment (E), GCA, and GCA × E. The SCA, and SCA × E effects were not significant for any of the disease severity variables. The GCA effects were more important than SCA for this set of inbred lines, suggesting that additive genetic effects are the most important sources of variation for this trait. Heterosis effects for resistance were estimated, and it was possible to identify specific hybrid combinations between lines which have high potential for genetic control of this pathogen. Results for both disease severity variables were practically identical, even though the PI method was more convenient to use.

scholarly journals Morpho-physiological Traits and Mineral Composition on Local Maize Population Growing in Agro Ecological Conditions in Kosova

2013 ◽  
Vol 5 (2) ◽  
pp. 232-237
Author(s):  
Sali ALIU ◽  
Imer RUSINOVCI ◽  
Shukri FETAHU ◽  
Kemajl BISILIMI
Keyword(s):  
Block Design ◽  
Physiological Traits ◽  
Cellulose Content ◽  
Maize Breeding ◽  
Maize Population ◽  
Maize Populations ◽  
Randomized Complete Block Design ◽  
Morphological And Physiological Traits ◽  
The Mean ◽  
Field And Laboratory Conditions

Twelve local maize populations were evaluated at the experimental farm, University of Prishtina, Kosovo. The study was conducted to assess the magnitude of genetic variation in local maize populations for different morphological-physiological and chemical composition under field and laboratory conditions. Randomized complete block design (RCBD) with three replications was used for laying out the experiment. The results showed that there were significant differences for most morphological and physiological traits under study. The mean grain yield of all populations was 102.96 g plant-1. The protein and oil contents ranged between 11.53 to 9.43% and 4.23 to 4.87% respectively. The cellulose content varied from 6.03 to 6.37%. There were also big differences regarding phenotypic correlations. The present study revealed considerable amount of diversity among the local maize populations which could be manipulated for further improvement in maize breeding.

scholarly journals Okra seedlings production in protected environment, testing substrates and producing fruits in field

2013 ◽  
Vol 31 (1) ◽  
pp. 08-14 ◽  
Author(s):  
Edilson Costa ◽  
Taynara G de Souza ◽  
Gleciane de L Benteo ◽  
Katiane SS Benett ◽  
Cleiton GS Benett
Keyword(s):  
Block Design ◽  
Joint Analysis ◽  
State University ◽  
Mato Grosso ◽  
Randomized Block Design ◽  
Randomized Design ◽  
Completely Randomized Design ◽  
Hot Weather ◽  
Favorable Conditions ◽  
Mato Grosso Do Sul

The okra grows well in hot weather, finding favorable conditions for development in Brazil. We evaluated the production of okra seedlings and productivity. The experiment was conducted in the experimental area of the State University of Mato Grosso do Sul, in Aquidauana. In the seedling phase we tested substrates (100% triturated cassava stems, 75% triturated cassava stems and 25% vermiculite, 50% triturated cassava stems and 50% vermiculite, 25% triturated cassava stems and 75% vermiculite and 100% vermiculite). These substrates were placed in two protected environments (nursery with black screen, 50% of shading, and aluminized screen, 50% of shading). Each environment was considered an experiment conducted in completely randomized design with eight replications. After that we realized joint analysis. In the field, a total of 10 treatments generated from combinations of environments and substrates (2 environments x 5 substrates) were distributed in a randomized block design with four replications. The average proportions of cassava stems and vermiculite may be suitable for okra seedlings. The results of shoot and total dry phytomass indicate that the aluminized screen can be recommended for okra seedlings production when the substrate with a 1:1 ratio is used. Seedlings grown on higher percentages of vermiculite anticipate production, while seedlings produced only in cassava stems tend to slow it down. The aluminized screen tends to increase the yield of okra seedlings. Average proportions of vermiculite and cassava stems for seedling production under aluminized screen, provide more fruits and yield of okra in Aquidauana.

scholarly journals Diallel Analysis for Area, Chlorophyll and Temperature of Flag Leaf in Bread Wheat under Well Watered and Drought Stress Conditions

2021 ◽  
Vol 13 (10) ◽  
pp. 45
Author(s):  
Naheif E. Mohamed ◽  
Ismail M. Bedawy ◽  
Yasser A. M. Hefny
Keyword(s):  
Drought Stress ◽  
Bread Wheat ◽  
Flag Leaf ◽  
Block Design ◽  
Diallel Analysis ◽  
Stress Conditions ◽  
F1 Hybrids ◽  
Gene Effects ◽  
Genetic Components ◽  
Additive Gene

To study genetic analysis of some physiological traits of drought stress in wheat using diallel techniques, an experiment was performed on ten bread wheat genotypes as parents and their 45 F1 hybrids in a randomized complete block design with three replicates under well-watered and drought stress conditions at the Research Farm of Faculty of Agriculture, Sohag University, Egypt during season of 2018/19. The results showed significant differences between the genotypes (G), Parents (P), F1 crosses, P vs. F1, GCA and SCA under well-watered and drought stress in the flag leaf area (FLA), flag leaf chlorophyll content (FLCC) and flag leaf temperature (FLT), except FLCC for F1 crosses exhibited insignificant differences. The significant differences were found in the interaction of SCA &times; Env., in all studied traits and GCA &times; Env., for FLT., indicating the involvement of both additive and dominance gene action in their inheritance. The most desirable heterotic effects were considered as the largest positive heterosis estimates for FLA and FLCC, and the lowest negative for FLT. The parent numbers P9, P8 and P3 were the best general combiner for FLA under normal irrigation and drought stress. While the parents P2, P7 and P9 were the best general combiner for FLCC, under normal irrigation and (P1, P2 and P3) under drought stress. Therefor the parents P1, P4 and P5 were the best general combiner for FLT under normal irrigation, also the P3, P4 and P5 were the best general combiner for FLT under drought stress conditions. Under normal irrigation and drought stress conditions as well as the combined data, the additive genetic components of variation (VA) in F1 &rsquo;s was much greater than dominance component (VD), as expressed by the (VA/VD) ratio which was more than unity for the FLA, and FLT under normal irrigation and their combined. This indicates that the additive gene effects in F1 crosses are more important than dominance and plays the major role in the inheritance of these studied traits.

scholarly journals Selección temprana de líneas S1 de maíz ricas en lisina: I probadores.

2016 ◽  
Vol 9 (2) ◽  
pp. 65
Author(s):  
María Cristina Vega ◽  
Enrique Navarro ◽  
José Espinoza ◽  
Gustavo A. Buciaga ◽  
José Luis Guerrero
Keyword(s):  
Grain Yield ◽  
Block Design ◽  
Agronomic Performance ◽  
Lysine Content ◽  
Fusarium Spp ◽  
Maize Breeding ◽  
High Lysine ◽  
Genetic Base ◽  
Randomized Complete Block Design ◽  
Normal Performance

This research involved ninety-six S1 maize lines with the opaque-2 gene that carne from populations 63 (26 lines), 65 (12 lines), and 68 (58 lines) from the CIMMYT maize breeding programo The S1 lines selected in the laboratory because of their high lysine content were crossed with five testers that had a different genetic base: a synthetic variety, two early lines derived from this variety, and two single intermediate crosses of normal performance. The test crosses were evaluated and compared with five control s (two commercial and three experimental hybrids) using a randomized complete block design in two sites in Mexico during 1992. The objecti ves of this research were to select SI lines in early generations according to their agronomic performance, grain lysine content, and GCA grain yield, and to compare testers' efficiency in discriminating S1 lines. On average, the SI lines of population 63 showed a greater grain yield as compared to that of populations 65 and 68 combined with all testers, except in the case of the synthetic tester YS- 201-M. A line from population 65 combined with tester B3 x B5 showed the highest grain yield (10,23 t ha-I), representing a superiority of 4% above the best commercial hybrid, AN- 447. A total ofthirty-one Sllines were selected based on their agronomic attributes and grain yield: 13, 14, and 4 from populations 63, 65 and 68 respectively]. Tester B3 x B5 tumed out to be the best line discriminator according to the following criteria: grain yield, percentage of ears damaged by Fusarium spp., and number of rotten ears.

scholarly journals Sensitivity and specificity of information criteria

2019 ◽  
Vol 21 (2) ◽  
pp. 553-565 ◽  
Author(s):  
John J Dziak ◽  
Donna L Coffman ◽  
Stephanie T Lanza ◽  
Runze Li ◽  
Lars S Jermiin
Keyword(s):  
Bayesian Information Criterion ◽  
Information Criterion ◽  
Information Criteria ◽  
The Other ◽  
Biological Research ◽  
Ratio Test ◽  
Relative Importance ◽  
Fields Of Study ◽  
Alternative Perspective ◽  
Practical Implications

Abstract Information criteria (ICs) based on penalized likelihood, such as Akaike’s information criterion (AIC), the Bayesian information criterion (BIC) and sample-size-adjusted versions of them, are widely used for model selection in health and biological research. However, different criteria sometimes support different models, leading to discussions about which is the most trustworthy. Some researchers and fields of study habitually use one or the other, often without a clearly stated justification. They may not realize that the criteria may disagree. Others try to compare models using multiple criteria but encounter ambiguity when different criteria lead to substantively different answers, leading to questions about which criterion is best. In this paper we present an alternative perspective on these criteria that can help in interpreting their practical implications. Specifically, in some cases the comparison of two models using ICs can be viewed as equivalent to a likelihood ratio test, with the different criteria representing different alpha levels and BIC being a more conservative test than AIC. This perspective may lead to insights about how to interpret the ICs in more complex situations. For example, AIC or BIC could be preferable, depending on the relative importance one assigns to sensitivity versus specificity. Understanding the differences and similarities among the ICs can make it easier to compare their results and to use them to make informed decisions.

scholarly journals Two-Hour Post-Load Plasma Glucose, a Biomarker to Improve the GRACE Score in Patients without Known Diabetes

Cardiology ◽  
2020 ◽  
Vol 145 (9) ◽  
pp. 553-561
Author(s):  
Sudipta Chattopadhyay ◽  
Anish George ◽  
Joseph John ◽  
Thozhukat Sathyapalan
Keyword(s):  
Plasma Glucose ◽  
Information Criteria ◽  
Prognostic Models ◽  
Ratio Test ◽  
Cardiac Events ◽  
Free Survival ◽  
Time Points ◽  
Coronary Syndrome ◽  
Akaike’S Information Criteria

Objective: To assess improvement in predictive performance of Global Registry of Acute Coronary Events risk score (GRS) by addition of a glucose matrix. Methods: 1,056 acute coronary syndrome (ACS) survivors without known diabetes had pre-discharge fasting (FPG) and 2-h post-load plasma glucose (2h-PG) measured. GRS was calculated. Major adverse cardiac events (MACE; death and non-fatal myocardial infarction) were recorded during follow-up. Cox proportional hazard regression predicted event-free survival. Likelihood ratio test, Akaike’s information criteria, continuous net reclassification index (NRI>0), and integrated discrimination improvement (IDI) were used to test the additional prognostic value of glycaemic indices over GRS. Results: During a median follow-up of 36.5 months, 211 MACEs (20.0%), 96 deaths (9.1%), and 115 non-fatal re-infarctions (10.9%), occurred. 2h-PG, but not FPG, independently predicted MACE-free survival at all time points (HR 1.08, 95% CI 1.03–1.13, p = 0.002, at 3 years). Risk of MACE increased by 8–11% with every 1 mmol/L rise in 2h-PG. 2h-PG significantly improved the prognostic models containing GRS. Models containing GRS and 2h-PG yielded lowest corrected Akaike’s information criteria compared to that with only GRS. 2h-PG, but not FPG, improved NRI>0 (NRI>0 0.169, p = 0.028 at 3 years) and IDI (IDI of 0.66%, p = 0.018 at 3 years) significantly at all time points during the follow-up. Conclusions: 2h-PG, but not FPG, improves performance of GRS-containing models in predicting post-ACS prognosis in the short to medium term.

scholarly journals Genetic evaluation of growth traits in Nellore cattle through multi-trait and random regression models

2018 ◽  
Vol 63 (No. 6) ◽  
pp. 212-221 ◽  
Author(s):  
B.B. Teixeira ◽  
R.R. Mota ◽  
R.B. Lôbo ◽  
L.P. Silva ◽  
A.P. Souza Carneiro ◽  
...  
Keyword(s):  
Random Effects ◽  
Variance Components ◽  
Regression Models ◽  
Growth Traits ◽  
Growth Curves ◽  
Genetic Evaluation ◽  
Information Criteria ◽  
Random Regression ◽  
Nellore Cattle ◽  
Heritability Estimates

We aimed to evaluate different orders of fixed and random effects in random regression models (RRM) based on Legendre orthogonal polynomials as well as to verify the feasibility of these models to describe growth curves in Nellore cattle. The proposed RRM were also compared to multi-trait models (MTM). Variance components and genetic parameters estimates were performed via REML for all models. Twelve RRM were compared through Akaike (AIC) and Bayesian (BIC) information criteria. The model of order three for the fixed curve and four for all random effects (direct genetic, maternal genetic, permanent environment, and maternal permanent environment) fits best. Estimates of direct genetic, maternal genetic, maternal permanent environment, permanent environment, phenotypic and residual variances were similar between MTM and RRM. Heritability estimates were higher via RRM. We presented perspectives for the use of RRM for genetic evaluation of growth traits in Brazilian Nellore cattle. In general, moderate heritability estimates were obtained for the majority of studied traits when using RRM. Additionally, the precision of these estimates was higher when using RRM instead of MTM. However, concerns about the variance components estimates in advanced ages via Legendre polynomial must be taken into account in future studies.

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