Quantitative genetics theory for genomic selection and efficiency of genotypic value prediction in open-pollinated populations

ABSTRACT: Quantitative genetics theory for genomic selection has mainly focused on additive effects. This study presents quantitative genetics theory applied to genomic selection aiming to prove that prediction of genotypic value based on thousands of single nucleotide polymorphisms (SNPs) depends on linkage disequilibrium (LD) between markers and QTLs, assuming dominance and epistasis. Based on simulated data, we provided information on dominance and genotypic value prediction accuracy, assuming mass selection in an open-pollinated population, all quantitative trait loci (QTLs) of lower effect, and reduced sample size. We show that the predictor of dominance value is proportional to the square of the LD value and to the dominance deviation for each QTL that is in LD with each marker. The weighted (by the SNP frequencies) dominance value predictor has greater accuracy than the unweighted predictor. The linear × linear, linear × quadratic, quadratic × linear, and quadratic × quadratic SNP effects are proportional to the corresponding linear combinations of epistatic effects for QTLs and the LD values. LD between two markers with a common QTL causes a bias in the prediction of epistatic values. Compared to phenotypic selection, the efficiency of genomic selection for genotypic value prediction increases as trait heritability decreases. The degree of dominance did not affect the genotypic value prediction accuracy and the approach to maximum accuracy is asymptotic with increases in SNP density. The decrease in the sample size from 500 to 200 did not markedly reduce the genotypic value prediction accuracy

Genomic-based-breeding tools for tropical maize improvement

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail

Parent Relationship Quality Buffers against the Effect of Peer Stressors on Depressive Symptoms from Middle Childhood to Adolescence.

During the transition to adolescence, several developmental trends converge to increase the importance of peer relationships, the likelihood of peer-related stressors, and the experience of depressive symptoms. Simultaneously, there are significant changes in parent-child relationships. The current study sought to evaluate whether positive relationship quality with parents continued to serve a protective effect by buffering the relationship between stressful life events, especially peer stress, and increases in depressive symptoms throughout the transition to adolescence. Participants in a large (N = 692) 2-site accelerated longitudinal study were recruited in 3rd, 6th, and 9th grade and followed every 3 months for 1 year. At baseline, parents and youth reported on parent-child relationship quality, and every 3 months thereafter reported on their levels of stressors and depressive symptoms. Parent relationship quality moderated the relationship of person-level fluctuations in peer stressors, such that there was a stronger association between peer stressors and increases in depressive symptoms in youth with lower levels of positive parental relationship quality. This effect was specific to peer stressors. These results suggest that low levels of parent relationship quality leave youth particularly vulnerable to the depressogenic effects of peer stressors from childhood through adolescence

Parent relationship quality buffers against the effect of peer stressors on depressive symptoms from middle childhood to adolescence.

During the transition to adolescence, several developmental trends converge to increase the importance of peer relationships, the likelihood of peer-related stressors, and the experience of depressive symptoms. Simultaneously, there are significant changes in parent-child relationships. The current study sought to evaluate whether positive relationship quality with parents continued to serve a protective effect by buffering the relationship between stressful life events, especially peer stress, and increases in depressive symptoms throughout the transition to adolescence. Participants in a large (N = 675), two-site accelerated longitudinal study were recruited in 3(rd), 6(th), & 9(th) grade and followed every 3 months for 1 year. At baseline parents and youth reported on parent-child relationship quality, and every three months thereafter reported on their levels of stressors and depressive symptoms. Parent relationship quality moderated the relationship of person-level fluctuations in peer stressors, such that there was a stronger association between peer stressors and increases in depressive symptoms in youth with lower levels of positive parental relationship quality. This effect was specific to peer stressors. These results suggest that low levels of parent relationship quality leave youth particularly vulnerable to the depressogenic effects of peer stressors from childhood through adolescence

On the accuracy in high dimensional linear models and its application to genomic selection

International audienceGenomic selection, a hot topic in genetics, consists in predicting breeding values of selection candidates, using a large number of genetic markers , due to the recent progress in molecular biology. One of the most popular method chosen by geneticists is Ridge regression. In this context, we focus on some predictive aspects of Ridge regression and present theoretical results regarding the accuracy criteria, i.e., the correlation between predicted value and true value. We show the influence of the singular values, the regularization parameter , and the projection of the signal on the space spanned by the rows of the design matrix. Asymptotic results, in a high dimensional framework, are also given, and we prove that the convergence to an optimal accuracy highly depends on a weighted projection of the signal on each subspace. We discuss also on how to improve the prediction. Last, illustrations on simulated and real data are proposed