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The Plant Genome Abstract - Original Research

AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example

 

This article in TPG

  1. Vol. 9 No. 3
    unlockOPEN ACCESS
     
    Received: Jan 25, 2016
    Accepted: June 10, 2016
    Published: September 1, 2016


    * Corresponding author(s): p.munoz@ufl.edu
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doi:10.3835/plantgenome2016.01.0009
  1. Rodrigo R. Amadeua,
  2. Catherine Cellonb,
  3. James W. Olmsteadb,
  4. Antonio A. F. Garciaa,
  5. Marcio F. R. Resende Jr.c and
  6. Patricio R. Muñoz *d
  1. a Dep. of Genetics, Luiz de Queiroz College of Agriculture, Univ. of Sao Paulo, Av. Padua Dias 11, P.O. Box 87, 13400-970, Piracicaba, SP, Brazil
    b Horticultural Sciences Dep., Institute of Food and Agricultural Sciences, Univ. of Florida, P.O. Box 110690, Gainesville, FL 32611, USA
    c RAPiD Genomics LLC, 756 2nd Avenue, Gainesville, FL, 32601, USA
    d Agronomy Dep., Institute of Food and Agricultural Sciences, Univ. of Florida, P.O. Box 110965, Gainesville, FL 32611, USA
Core Ideas:
  • We developed an R package for autopolyploids to construct the relationship matrix.
  • We estimated the level and effect of double reduction in blueberry.
  • The package is unique as it can create A-matrices for different levels of ploidy.
  • The package can create A-matrices for different levels of double reduction

Abstract

Progress in the rate of improvement in autopolyploid species has been limited compared with diploids, mainly because software and methods to apply advanced prediction and selection methodologies in autopolyploids are lacking. The objectives of this research were to (i) develop an R package for autopolyploids to construct the relationship matrix derived from pedigree information that accounts for autopolyploidy and double reduction and (ii) use the package to estimate the level and effect of double reduction in an autotetraploid blueberry breeding population with extensive pedigree information. The package is unique, as it can create A-matrices for different levels of ploidy and double reduction, which can then be used by breeders to fit mixed models in the context of predicting breeding values (BVs). Using the data from this blueberry population, we found for all the traits that tetrasomic inheritance creates a better fit than disomic inheritance. In one of the five traits studied, the level of double reduction was different from zero, decreasing the estimated heritability, but it did not affect the prediction of BVs. We also discovered that different depths of pedigree would have significant implications on the estimation of double reduction using this approach. This freely available R package is available for autopolyploid breeders to estimate the level of double reduction present in their populations and the impact in the estimation of genetic parameters as well as to use advanced methods of prediction and selection.

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