Abstract
Sour passion fruit is an economically important tropical fruit crop with little explored genetic potential. This study aimed to provide breeders with essential estimates of genomic breeding values in economically important traits in passion fruit, using Bayesian models which may contribute to the implementation of Genomic Selection and develop new strategies for the continuity of sour passion fruit breeding programs. For this, the following Bayesian models were tested using 183 polymorphic marks: Bayesian Ridge regression, Bayes A, Bayes B, Bayes B2, Bayes Cπ and Bayesian Lasso for estimation of genomic breeding values. To achieve this, ninety-five full-sib progenies derived from the third cycle of recurrent selection of the sour passion fruit (Passiflora edulis Sims.) at Universidade Estadual do Norte Fluminense Darcy Ribeiro—UENF were used and eight fruit yield (number of fruit, total yield, mean fruit weight, fruit length, fruit width) and quality(percent pulp, skin thickness, soluble solids) traits were assessed. The Bayes Cπ (smaller deviance information criterion) yield the best genetic predictions for almost all traits. Genetic correlations in this study indicate that the number of fruit can be used as a proxy for yield. The values of genomic heritability obtained were high and ranged from 0.62 to 0.76 and predict accuracy ranged from 0.55 to 0.75, so we can to speculate that the use of two replicates in the present study was an adequate amount to obtain phenotypic mean, which was used to adjust the genomic prediction model.
Similar content being viewed by others
References
Bernardo R, Yu J (2007) Prospects for genome wide selection for quantitative traits in maize. Crop Sci 47(3):1082–1090
Chen Y, Lübberstedt T (2010) Molecular basis of trait correlations. Trends Plant Sci 15:454–461
Coelho AA, Cenci SA, de Resende ED (2010) Qualidade do suco de maracujá-amarelo em diferentes pontos de colheita e após o amadurecimento. Ciência e Agrotecnologia 34(3):722–729
de los Campos G, Naya H, Gianola D, Crossa J, Legarra A (2009) Prediction quantitative traits with regression models for dense molecular markers and pedigree. Genetics 182:375–385
de los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MPL (2013) Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics 193:327–345
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Geweke J (1992) Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments. In: Bernardo JM, Berger J, Dawid AP, Smith AFM (eds) Bayesian statistics, vol 4. Oxford University Press, Oxford, pp 169–193
Gianola D (2013) Priors in whole-genome regression: the Bayesian alphabet returns. Genetics 194:573–596
Gianola D, de los Campos G, Hill WG, Manfredi E, Fernando RL (2009) Additive genetic variability and the Bayesian alphabet. Genetics 183:347–363
Gonçalves GM, Viana AP, Pereira MG, Bezerra Neto FV, Amaral AT, Pereira TNS (2008) Phenotypic and genetic additive correlations in yellow passion fruit obtained by design I. Ciência e Agrotecnologia 32:1413–1418
Grattapaglia D, Resende MDV (2011) Genomic selection in forest tree breeding. Tree Genet Genomes 7(2):241–255
Habier D, Fernando RL, Kizilkaya K, Garrick DJ (2011) Extension of the Bayesian alphabet for genomic selection. BMC Bioinform 12:186 1–12. http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-186
Kumar S, Chagné D, Bink MCAM, Volz RK, Whitwork C (2012) Genomic selection for fruit quality traits in apple (Malus × domestica Borkh). PLoS ONE 7:e36674
Legarra A, Robert-Granie C, Manfredi E, Elsen JM (2008) Performance of genomic selection in mice. Genetics 180:611–618
Martins MR, Oliveira JC, Di Mauro AO, Silva PC (2003) Evaluation of sweet passion fruit (Passiflora alata Curtis) populations obtained by open polinization. Rev Bras Frutic 25(1):111–114
Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
Moraes MC, Geraldi IO, Matta FP, Vieira MLC (2005) Genetic and phenotypic parameter estimates for yield and fruit quality traits from a single wide cross in yellow passion fruit. HortScience 40:1978–1981
Morgado MAD, Santos CEM, Linhales H, Bruckner CH (2010) Correlações fenotípicas em características fisicoquímicas do maracujazeiro-azedo. Acta Agron 59(4):457–461
Oliveira EJ (2006) Development of microsatellite markers and their use for the generation and integration of genetic maps of yellow passion fruit (Passiflora edulis Sims f. flavicarpa Deg.) PhD Thesis. (Genetics and Plant Breeding), ESALQ, São Paulo
Oliveira EJ, Santos VS, Lima DS, Machado ML, Lucena RS, Motta TBN (2011) Genotypic and phenotypic correlation estimates from passion fruit germplasm. Bragantia 70(2):255–261
Park T, Casella G (2008) The bayesian LASSO. J Am Stat Assoc 103:681–686
Pérez P, de los Campos G (2014) Genome-wide regression & prediction with the BGLR statistical package. Genetics 198(2):483–495
R Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, http://www.R-project.org
Resende MDV, Lopes PS, Silva RL, Pires IL (2008) Seleção genômica ampla (GWS) e maximização da eficiência do melhoramento genético. Pesqui Florest Bras 56:63–77
Resende MDV, Silva FF, Lopes PS, Azevedo CF (2012a) Seleção genômica ampla (GWS) via modelos mistos (REML/BLUP), inferência Bayesiana (MCMC), Regressão aleatória multivariada (RRM) e estatística espacial. Universidade Federal de Viçosa, Viçosa, p 291
Resende MFR, Muñoz P, Acosta JJ, Peter GF, Davis JM, Grattapaglia D, Resende MDV, Kirst M (2012b) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytol 193:617–624
Silva FF, Rosa GJ, Guimarães SE, Lopes PS, de los Campos G (2011) Three-step Bayesian factor analysis applied to QTL detection in crosses between outbred pig populations. Livest Sci 142(1):210–215
Silva FHL, Muñoz PR, Vincent CI, Viana AP (2016) Generating relevant information for breeding Passiflora edulis: genetic parameters and population structure. Euphytica 208:609–619
Silva FHL, Viana AP, Santos EA, Freitas JCO, Rodrigues DL, Amaral Júnior AT (2017) Prediction of genetic gains by selection indexes and REML/BLUP methodology in a population of sour passion fruit under recurrent selection. Acta Sci 39(2):183–190
Smith BJ (2007) boa: an R package for MCMC output convergence assessment and posterior inference. J Stat Softw 21:1–37
Spiegelhalter DJ, Best NG, Carlin BP, Van der Linde A (2002) Bayesian measures of model complexity and fit. J R Stat Soc Ser B 64:583–639
Tibshirani R (1996) Regression shrinkage and selection via the lasso. J R Stat Soc Ser B 58(1):267–288 (Methodological)
Usai MG, Goddard ME, Hayes BJ (2009) LASSO whit cross-validation for genomic selection. Genet Res 91:427–436
Viana AP, Resende MDV (2014) Genética quantitativa no melhoramento de fruteiras, 10th edn. Interciência, Rio de Janeiro, p 280p
Viana AP, Resende MDV, Summaira R, Walker MA (2016) Genome selection in fruit breeding: application to table grapes. Sci Agricola 73(2):142–149
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Viana, A.P., de Lima e Silva, F.H., Glória, L.S. et al. Implementing genomic selection in sour passion fruit population. Euphytica 213, 228 (2017). https://doi.org/10.1007/s10681-017-2020-3
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10681-017-2020-3