Genomic prediction of trait segregation in a progeny population: a case study of Japanese pear (Pyrus pyrifolia)

BMC Genetics

Toshiya Yamamoto¹  Toshihiro Saito¹  Norio Takada¹  Shingo Terakami¹  Takeshi Hayashi³  Hiroyoshi Iwata² 

[1] NARO Institute of Fruit Tree Science, 2-1 Fujimoto, Ibaraki, 305-8605, Tsukuba, Japan;Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, 113-8657, Tokyo, Japan;NARO Agricultural Research Center, 3-1-1 Kannondai, Ibaraki, 305-8666, Tsukuba, Japan

关键词: Ordinal categorical scores;    Genome-wide markers;    Markov Chain Monte Carlo (MCMC);    Bayesian modeling;    Segregation simulation;    Selection of a parental combination;    Genomic selection;   

Others  :  1086702
DOI  :  10.1186/1471-2156-14-81

 received in 2013-02-15, accepted in 2013-09-05,  发布年份 2013

【 摘 要 】

Background

In cross breeding, it is important to choose a good parental combination that has high probability of generating offspring with desired characteristics. This study examines a method for predicting the segregation of target traits in a progeny population based on genome-wide markers and phenotype data of parental cultivars.

Results

The proposed method combines segregation simulation and Bayesian modeling for genomic selection. Marker segregation in a progeny population was simulated based on parental genotypes. Posterior marker effects sampled via Markov Chain Monte Carlo were used to predict the segregation pattern of target traits. The posterior distribution of the proportion of progenies that fulfill selection criteria was calculated and used for determining a promising cross and the necessary size of the progeny population. We applied the proposed method to Japanese pear (Pyrus pyrifolia Nakai) data to demonstrate the method and to show how it works in the selection of a promising cross. Verification using an actual breeding population suggests that the segregation of target traits can be predicted with reasonable accuracy, especially in a highly heritable trait. The uncertainty in predictions was reflected on the posterior distribution of the proportion of progenies that fulfill selection criteria. A simulation study based on the real marker data of Japanese pear cultivars also suggests the potential of the method.

Conclusions

The proposed method is useful to provide objective and quantitative criteria for choosing a parental combination and the breeding population size.

【 授权许可】

   
2013 Iwata et al.; licensee BioMed Central Ltd.

【 图 表 】

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