Identifying and testing marker‐trait associations for growth and phenology in three pine species: implications for genomic prediction

The present study aimed to improve the accuracy of genomic prediction of 16 agronomic traits in a diverse bread wheat (Triticum aestivum L.) germplasm under terminal drought stress and well-watered conditions in semi-arid environments. An association panel including 87 bread wheat cultivars and 199 landraces from Iran bread wheat germplasm was planted under two irrigation systems in semi-arid climate zones. The whole association panel was genotyped with 9047 single nucleotide polymorphism markers using the genotyping-by-sequencing method. A number of 23 marker-trait associations were selected for traits under each condition, whereas 17 marker-trait associations were common between terminal drought stress and well-watered conditions. The identified marker-trait associations were mostly single nucleotide polymorphisms with minor allele effects. This study examined the effect of population structure, genomic selection method (ridge regression-best linear unbiased prediction, genomic best-linear unbiased predictions, and Bayesian ridge regression), training set size, and type of marker set on genomic prediction accuracy. The prediction accuracies were low (-0.32) to moderate (0.52). A marker set including 93 significant markers identified through genome-wide association studies with P values ≤ 0.001 increased the genomic prediction accuracy for all traits under both conditions. This study concluded that obtaining the highest genomic prediction accuracy depends on the extent of linkage disequilibrium, the genetic architecture of trait, genetic diversity of the population, and the genomic selection method. The results encouraged the integration of genome-wide association study and genomic selection to enhance genomic prediction accuracy in applied breeding programs.

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Multi-model genome-wide association and genomic prediction analysis of 16 agronomic, physiological and quality related traits in ICARDA spring wheat

Euphytica ◽

10.1007/s10681-021-02933-6 ◽

2021 ◽

Vol 217 (11) ◽

Author(s):

Admas Alemu ◽

Sufian Suliman ◽

Adel Hagras ◽

Sherif Thabet ◽

Ayed Al-Abdallat ◽

...

Keyword(s):

Heat Stress ◽

Heat Tolerance ◽

Spring Wheat ◽

Genomic Prediction ◽

Marker Assisted Selection ◽

Genome Wide Association ◽

Genome Wide ◽

Chromosome Arm ◽

Yield Quality ◽

Trait Associations

AbstractIdentification and exploration of the genetic architecture of traits related to yield, quality, and drought and heat tolerance is important for yield and quality improvement of wheat through marker-assisted selection. One hundred and ninety-two spring wheat genotypes were tested at two heat-stress locations in Sudan (Wad Medani and Dongula), a drought stress site in Morocco (Marchouch) and a site with high yield potential in Egypt (Sids) in replicated trials during the 2015–2016 and 2016–2017 cropping seasons. A total of 10,577 single nucleotide polymorphism markers identified from the 15 K wheat SNP assay were used in a genome-wide association (GWA) study and genomic prediction for 16 phenotypic traits related to yield, quality and drought and heat tolerance. Significant marker-trait associations were detected across GWAS models for all traits. Most detected marker-trait associations (MTAs) were environment-specific, signifying the presence of high quantitative trait loci-by-environment (QTL x E) interaction. Chromosome arm 5AL had significant multi-model MTAs for grain yield and yield-related traits at the heat-stress locations. Highly significant QTLs were detected on chromosome 2D for waxiness. Homoeologous group 2 and 6 chromosomes were with significant MTAs for grain protein content, gluten content, alveograph strength and Zeleny sedimentation test while chromosome arm 3BL was significant for both Z and W traits. Genomic prediction analysis with ridge regression-best linear unbiased prediction model estimated the breeding values of the studied traits with prediction accuracies ranging from 0.16 for leaf rolling to 0.72 for peduncle length. The identified QTLs could be targeted for marker-assisted selection or further studies aimed at fine mapping and cloning the causative genes and detecting favorable haplotypes with positive effects for agronomic, physiological or quality-related traits.

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Red Heart Disease in Pines Caused by Porodaedalea (Phellinus) pini in Florida

EDIS ◽

10.32473/edis-fr425-2019 ◽

2020 ◽

Vol 2020 (1) ◽

pp. 3

Author(s):

Yin-Tse Huang ◽

Jeffrey Eickwort ◽

Jiri Hulcr

Keyword(s):

Heart Disease ◽

Forest Resources ◽

Fact Sheet ◽

Cavity Nesting ◽

Pine Species

All pine species in Florida are susceptible to red heart disease. The disease can decrease timber value and weaken trees, making them threats to people and property. In forests, however, the same disease can be beneficial to cavity-nesting animals like red-cockaded woodpeckers. This 3-page fact sheet written by Yin-Tse Huang, Jeffrey Eickwort, and Jiri Hulcr and published by the UF/IFAS School of Forest Resources and Conservation describes the disease and provides some tips to manage it in areas where it could cause problems for people.http://edis.ifas.ufl.edu/fr425

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Spatio-temporal approach for identification of critical conservation areas: a case study with two pine species from a threatened temperate forest in Mexico

Biodiversity and Conservation ◽

10.1007/s10531-019-01767-y ◽

2019 ◽

Vol 28 (7) ◽

pp. 1863-1883 ◽

Cited By ~ 3

Author(s):

Agustín Molina Sánchez ◽

Patricia Delgado ◽

Antonio González-Rodríguez ◽

Clementina González ◽

A. Francisco Gómez-Tagle Rojas ◽

...

Keyword(s):

Temperate Forest ◽

Conservation Areas ◽

Spatio Temporal ◽

Pine Species

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Genomic prediction ability for carcass composition indicator traits in Nellore cattle

Livestock Science ◽

10.1016/j.livsci.2021.104421 ◽

2021 ◽

Vol 245 ◽

pp. 104421

Author(s):

Rosiane P. Silva ◽

Rafael Espigolan ◽

Mariana P. Berton ◽

Raysildo B. Lôbo ◽

Cláudio U. Magnabosco ◽

...

Keyword(s):

Genomic Prediction ◽

Carcass Composition ◽

Prediction Ability ◽

Nellore Cattle ◽

Indicator Traits

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The look ahead trace back optimizer for genomic selection under transparent and opaque simulators

Scientific Reports ◽

10.1038/s41598-021-83567-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Fatemeh Amini ◽

Felipe Restrepo Franco ◽

Guiping Hu ◽

Lizhi Wang

Keyword(s):

Genomic Selection ◽

Genetic Gain ◽

Genomic Prediction ◽

In Planta ◽

Data Set ◽

Look Ahead ◽

Trace Back ◽

New Variant ◽

The Look ◽

Partially Observable

AbstractRecent advances in genomic selection (GS) have demonstrated the importance of not only the accuracy of genomic prediction but also the intelligence of selection strategies. The look ahead selection algorithm, for example, has been found to significantly outperform the widely used truncation selection approach in terms of genetic gain, thanks to its strategy of selecting breeding parents that may not necessarily be elite themselves but have the best chance of producing elite progeny in the future. This paper presents the look ahead trace back algorithm as a new variant of the look ahead approach, which introduces several improvements to further accelerate genetic gain especially under imperfect genomic prediction. Perhaps an even more significant contribution of this paper is the design of opaque simulators for evaluating the performance of GS algorithms. These simulators are partially observable, explicitly capture both additive and non-additive genetic effects, and simulate uncertain recombination events more realistically. In contrast, most existing GS simulation settings are transparent, either explicitly or implicitly allowing the GS algorithm to exploit certain critical information that may not be possible in actual breeding programs. Comprehensive computational experiments were carried out using a maize data set to compare a variety of GS algorithms under four simulators with different levels of opacity. These results reveal how differently a same GS algorithm would interact with different simulators, suggesting the need for continued research in the design of more realistic simulators. As long as GS algorithms continue to be trained in silico rather than in planta, the best way to avoid disappointing discrepancy between their simulated and actual performances may be to make the simulator as akin to the complex and opaque nature as possible.

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Genomic prediction using training population design in interspecific soybean populations

Molecular Breeding ◽

10.1007/s11032-021-01203-6 ◽

2021 ◽

Vol 41 (2) ◽

Author(s):

Eduardo Beche ◽

Jason D. Gillman ◽

Qijian Song ◽

Randall Nelson ◽

Tim Beissinger ◽

...

Keyword(s):

Genomic Prediction ◽

Training Population ◽

Population Design

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On the use of whole-genome sequence data for across-breed genomic prediction and fine-scale mapping of QTL

Genetics Selection Evolution ◽

10.1186/s12711-021-00607-4 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Theo Meuwissen ◽

Irene van den Berg ◽

Mike Goddard

Keyword(s):

Variable Selection ◽

Genome Sequence ◽

Genomic Prediction ◽

Milk Fat ◽

Genotype Imputation ◽

Whole Genome Sequence ◽

Genomic Relationship Matrix ◽

Polygenic Effect ◽

Relationship Matrix ◽

Whole Genome

Abstract Background Whole-genome sequence (WGS) data are increasingly available on large numbers of individuals in animal and plant breeding and in human genetics through second-generation resequencing technologies, 1000 genomes projects, and large-scale genotype imputation from lower marker densities. Here, we present a computationally fast implementation of a variable selection genomic prediction method, that could handle WGS data on more than 35,000 individuals, test its accuracy for across-breed predictions and assess its quantitative trait locus (QTL) mapping precision. Methods The Monte Carlo Markov chain (MCMC) variable selection model (Bayes GC) fits simultaneously a genomic best linear unbiased prediction (GBLUP) term, i.e. a polygenic effect whose correlations are described by a genomic relationship matrix (G), and a Bayes C term, i.e. a set of single nucleotide polymorphisms (SNPs) with large effects selected by the model. Computational speed is improved by a Metropolis–Hastings sampling that directs computations to the SNPs, which are, a priori, most likely to be included into the model. Speed is also improved by running many relatively short MCMC chains. Memory requirements are reduced by storing the genotype matrix in binary form. The model was tested on a WGS dataset containing Holstein, Jersey and Australian Red cattle. The data contained 4,809,520 genotypes on 35,549 individuals together with their milk, fat and protein yields, and fat and protein percentage traits. Results The prediction accuracies of the Jersey individuals improved by 1.5% when using across-breed GBLUP compared to within-breed predictions. Using WGS instead of 600 k SNP-chip data yielded on average a 3% accuracy improvement for Australian Red cows. QTL were fine-mapped by locating the SNP with the highest posterior probability of being included in the model. Various QTL known from the literature were rediscovered, and a new SNP affecting milk production was discovered on chromosome 20 at 34.501126 Mb. Due to the high mapping precision, it was clear that many of the discovered QTL were the same across the five dairy traits. Conclusions Across-breed Bayes GC genomic prediction improved prediction accuracies compared to GBLUP. The combination of across-breed WGS data and Bayesian genomic prediction proved remarkably effective for the fine-mapping of QTL.

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Optimal breeding-value prediction using a Sparse Selection Index

Genetics ◽

10.1093/genetics/iyab030 ◽

2021 ◽

Author(s):

Marco Lopez-Cruz ◽

Gustavo de los Campos

Keyword(s):

Sample Size ◽

Dna Sequences ◽

Genomic Prediction ◽

Prediction Accuracy ◽

Regularization Parameter ◽

Selection Index ◽

Prediction Method ◽

Training Data ◽

Breeding Value ◽

Data Set

Abstract Genomic prediction uses DNA sequences and phenotypes to predict genetic values. In homogeneous populations, theory indicates that the accuracy of genomic prediction increases with sample size. However, differences in allele frequencies and in linkage disequilibrium patterns can lead to heterogeneity in SNP effects. In this context, calibrating genomic predictions using a large, potentially heterogeneous, training data set may not lead to optimal prediction accuracy. Some studies tried to address this sample size/homogeneity trade-off using training set optimization algorithms; however, this approach assumes that a single training data set is optimum for all individuals in the prediction set. Here, we propose an approach that identifies, for each individual in the prediction set, a subset from the training data (i.e., a set of support points) from which predictions are derived. The methodology that we propose is a Sparse Selection Index (SSI) that integrates Selection Index methodology with sparsity-inducing techniques commonly used for high-dimensional regression. The sparsity of the resulting index is controlled by a regularization parameter (λ); the G-BLUP (the prediction method most commonly used in plant and animal breeding) appears as a special case which happens when λ = 0. In this study, we present the methodology and demonstrate (using two wheat data sets with phenotypes collected in ten different environments) that the SSI can achieve significant (anywhere between 5-10%) gains in prediction accuracy relative to the G-BLUP.

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Stand-level biomass models for predicting C stock for the main Spanish pine species

Forest Ecosystems ◽

10.1186/s40663-021-00308-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Ana Aguirre ◽

Miren del Río ◽

Ricardo Ruiz-Peinado ◽

Sonia Condés

Keyword(s):

Form Factor ◽

Pinus Halepensis ◽

Dry Weight ◽

Pinus Nigra ◽

Carbon Stocks ◽

Tree Size ◽

Pine Forests ◽

Stand Volume ◽

Biomass Models ◽

Pine Species

Abstract Background National and international institutions periodically demand information on forest indicators that are used for global reporting. Among other aspects, the carbon accumulated in the biomass of forest species must be reported. For this purpose, one of the main sources of data is the National Forest Inventory (NFI), which together with statistical empirical approaches and updating procedures can even allow annual estimates of the requested indicators. Methods Stand level biomass models, relating the dry weight of the biomass with the stand volume were developed for the five main pine species in the Iberian Peninsula (Pinus sylvestris, Pinus pinea, Pinus halepensis, Pinus nigra and Pinus pinaster). The dependence of the model on aridity and/or mean tree size was explored, as well as the importance of including the stand form factor to correct model bias. Furthermore, the capability of the models to estimate forest carbon stocks, updated for a given year, was also analysed. Results The strong relationship between stand dry weight biomass and stand volume was modulated by the mean tree size, although the effect varied among the five pine species. Site humidity, measured using the Martonne aridity index, increased the biomass for a given volume in the cases of Pinus sylvestris, Pinus halepensis and Pinus nigra. Models that consider both mean tree size and stand form factor were more accurate and less biased than those that do not. The models developed allow carbon stocks in the main Iberian Peninsula pine forests to be estimated at stand level with biases of less than 0.2 Mg∙ha− 1. Conclusions The results of this study reveal the importance of considering variables related with environmental conditions and stand structure when developing stand dry weight biomass models. The described methodology together with the models developed provide a precise tool that can be used for quantifying biomass and carbon stored in the Spanish pine forests in specific years when no field data are available.

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