Multi-trait genomic prediction for nitrogen response indices in tropical maize hybrids

Lyra, Danilo Hottis; Mendonça, Leandro de Freitas; Galli, Giovanni; Alves, Filipe Couto; Granato, Ítalo Stefanine Correia; Fritsche‐Neto, Roberto

doi:10.1007/s11032-017-0681-1

Cited by 53 publications

(47 citation statements)

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“…Principal Component Analysis (PCA) and Admixture Clustering revealed the existence of two subpopulations in the inbred lines germplasm [18,31]. Additionally, according to Morosini et al [18], the panel presents a mean length of LD decay of 80-100 kb (r 2 = 0.13).…”

Section: Genomic Datamentioning

confidence: 95%

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On the usefulness of parental lines GWAS for predicting low heritability traits in tropical maize hybrids

et al. 2020

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Genome-wide association studies (GWAS) is one of the most popular methods of studying the genetic control of traits. This methodology has been intensely performed on inbred genotypes to identify causal variants. Nonetheless, the lack of covariance between the phenotype of inbred lines and their offspring in cross-pollinated species (such as maize) raises questions on the applicability of these findings in a hybrid breeding context. To address this topic, we incorporated previously reported parental lines GWAS information into the prediction of a low heritability trait in hybrids. This was done by marker-assisted selection based on significant markers identified in the lines and by genomic prediction having these markers as fixed effects. Additive-dominance GWAS of hybrids, a non-conventional procedure, was also performed for comparison purposes. Our results suggest that incorporating information from parental inbred lines GWAS led to decreases in the predictive ability of hybrids. Correspondingly, inbred lines and hybrids-based GWAS yielded different results. These findings do not invalidate GWAS on inbred lines for selection purposes, but mean that it may not be directly useful for hybrid breeding. OPEN ACCESSCitation: Galli G, Alves FC, Morosini JS, Fritsche-Neto R (2020) On the usefulness of parental lines GWAS for predicting low heritability traits in tropical maize hybrids. PLoS ONE 15(2): e0228724. https://doi.org/10.1371/journal.

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Section: Genomic Datamentioning

confidence: 95%

“…We added to this finding further functional polymorphisms that control the trait (Fig 2, Table 1). The aspects of genetic architecture, the high number of alleles, and low heritability [18,31] make it hard to predict and select superior genotypes.…”

Section: Implications On Cross-pollination Breeding For Low Heritabilmentioning

confidence: 99%

On the usefulness of parental lines GWAS for predicting low heritability traits in tropical maize hybrids

et al. 2020

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“…However, the limitations due to the small number of hybrids and the relatedness among our parental set may have influenced our results. For instance, in studies with larger panels of hybrids, a superior overall performance of the nonlinear GK model relative to GBLUP has been observed (Lyra et al, 2017;Cuevas et al, 2018). In this sense, the use of GK proposed in our study, when applied to other data sets, could show better results in comparison to the use of GB, as initially proposed by Acosta-Pech et al 2017and Massman et al (2013).…”

Section: Hybrid Performance Under a Brasilense Inoculation Can Be Prsupporting

confidence: 58%

“…For this, the diallel mating design can be a useful approach, since it determines the genetic control and the relative proportion of additive and non-additive genetic variation associated with the trait. Moreover, the genomic prediction of non-phenotyped genotypes has been routinely implemented in maize breeding programs and is the object of study of several authors (Sousa et al, 2017;Lyra et al, 2017). To our knowledge, there are no reports about the use of this approach for the traits related to the maize responsiveness to PGPB as Azospirillum sp., which are laborious and time-consuming for the mensuration.…”

Section: Introductionmentioning

confidence: 99%

Maize responsiveness to <i>Azospirillum brasilense</i>: insights into genetic control and genomic prediction

Vidotti¹

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Maize responsiveness to Azospirillum brasilense: insights into genetic control and genomic prediction The inoculation with Azospirillum brasilense is one of the main strategies to supplement the inorganic inputs of nitrogen (N) and to increase the root development in maize. However, the beneficial inoculation effects are not always reached, which, in part, is due to genotypic variation in the plant host, resulting in different degrees of outcome. In this context, we aimed to study the genetic control and genomic prediction of maize traits related to the responsiveness to A. brasilense inoculation. For this, 118 maize hybrids were conducted under N stress and N stress plus A. brasilense treatments in controlled conditions over 2016 and 2017 seasons. We evaluated root and shoot traits and performed diallel analyses, association mapping, and genomic prediction methods considering 59,215 Single-Nucleotide Polymorphism (SNP) markers. Our results revealed a quantitative inheritance of the partnership-related maize traits, with both additive and non-additive genetic effects involved in the genetic control. Furthermore, several candidate genes were identified for the maize-A. brasilense association, especially with heterozygous (dis)advantage effects. In general, the prediction accuracies were higher mostly for the inoculated treatment compared to the non-inoculated. Finally, our findings enable a deeper understanding towards the genetic basis of the maize responsiveness to A. brasilense and may support plant breeders to establish selection strategies aiming the development of superior genotypes for this association.

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“…Through this approach, it is possible to use traits with higher heritability to improve the power to predict the others trait (Bauer and Léon, 2008;Dos Santos et al, 2016;Fernandes et al, 2018). It has been successfully implemented using single by single trait (Jia and Jannink, 2012;Guo et al, 2014) or indices (Schulthess et al, 2016;Lyra et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Tropical forage breeding from classic to new genomic tools: an example with interspecific tetraploid <i>Urochloa</i> spp. hybrids

Matias¹

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Multi-trait genomic prediction for nitrogen response indices in tropical maize hybrids

Cited by 53 publications

References 50 publications

On the usefulness of parental lines GWAS for predicting low heritability traits in tropical maize hybrids

On the usefulness of parental lines GWAS for predicting low heritability traits in tropical maize hybrids

Maize responsiveness to <i>Azospirillum brasilense</i>: insights into genetic control and genomic prediction

Tropical forage breeding from classic to new genomic tools: an example with interspecific tetraploid <i>Urochloa</i> spp. hybrids

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