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Genome prediction accuracy of common bean via Bayesian models

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EnglishWe aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits “stay-green” (SG), plant architecture (PA), grain aspect (GA) and grain… Click to show full abstract

EnglishWe aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits “stay-green” (SG), plant architecture (PA), grain aspect (GA) and grain yield (GY) in common bean through Bayesian models. These models were compared in terms of prediction accuracy and ability for heritability estimation for each one of the mentioned traits. A total of 80 cultivars were genotyped for 377 SNP markers, whose effects were estimated by five different Bayesian models: Bayes A (BA), B (BB), C (BC), LASSO (BL) e Ridge regression (BRR). Although, prediction accuracies calculated by means of cross-validation have been similar within each trait, the BB model stood out for the trait SG, whereas the BRR was indicated for the remaining traits. The heritability estimates for the traits SG, PA, GA and GY were 0.61, 0.28, 0.32 and 0.29, respectively. In summary, the Bayesian methods applied here were effective and ease to be implemented. The used SNP markers can help in the early selection of promising genotypes, since incorporating genomic information increase the prediction accuracy of the estimated genetic merit. Key words: Phaseolus vulgaris; SNP markers; cross-validation portuguesObjetivou-se incorporar informacoes genomicas de marcadores SNP (“single nucleotide polymorphism”) na avaliacao genetica das caracteristicas “stay-green” (SG), arquitetura de planta (AP), aspecto de graos (AG) e produtividade de graos (PG) em feijoeiro-comum via modelos Bayesianos. Estes modelos foram comparados quanto a acuracia de predicao e habilidade de estimacao da herdabilidade para cada caracteristica. Utilizaram-se informacoes de 80 cultivares genotipadas para 377 marcadores SNP, cujos efeitos de substituicao alelica foram estimados por meio de cinco diferentes modelos Bayesianos: Bayes A (BA), B (BB), C (BC), LASSO (BL) e regressao “ridge” (BRR). Embora as acuracias de predicao calculadas por meio de analise de validacao cruzada tenham sido similares dentro de cada caracteristica, o modelo BB se destacou para a caracteristica SG, enquanto o modelo BRR foi indicado para as demais. As herdabilidades estimadas para SG, AP, AG e PG foram, respectivamente, 0,61, 0,28, 0,32 e 0,29. Em resumo, os metodos contemplados mostraram-se efetivos e de facil implementacao. O conjunto de marcadores utilizado pode auxiliar na selecao precoce de genotipos promissores, uma vez que a incorporacao de informacoes genomicas aumenta a acuracia de predicao do merito genetico estimado. Palavras-chave: Phaseolus vulgaris; marcadores SNP; validacao cruzada

Keywords: bayesian models; prediction accuracy; snp; common bean; prediction

Journal Title: Ciencia Rural
Year Published: 2018

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