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This article in TPG

  1. Vol. 5 No. 3, p. 103-113
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    Received: June 4, 2012
    Published: December 12, 2012


    * Corresponding author(s): jesse.poland@ars.usda.gov
    jpoland@ksu.edu
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doi:10.3835/plantgenome2012.06.0006

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

  1. Jesse Poland a,
  2. Jeffrey Endelmanc,
  3. Julie Dawsond,
  4. Jessica Rutkoskid,
  5. Shuangye Wub,
  6. Yann Manese,
  7. Susanne Dreisigackere,
  8. José Crossae,
  9. Héctor Sánchez-Villedae,
  10. Mark Sorrellsd and
  11. Jean-Luc Janninkc
  1. a USDA-ARS and Dep. of Agronomy, Kansas State Univ. (KSU), 4011 Throckmorton Hall, Manhattan KS, 66506
    c USDA-ARS R.W. Holley Center, Cornell Univ., Ithaca, NY 14853
    d Dep. of Plant Breeding and Genetics, Cornell Univ., 240 Emerson Hall, Ithaca NY 14853
    b Dep. of Agronomy, Kansas State Univ., 4008 Throckmorton Hall, Manhattan KS, 66506
    e International Maize and Wheat Improvement Center (CIMMYT), Int. Apdo. Postal 6-641, 06600 Mexico, DF, Mexico

Abstract

Genomic selection (GS) uses genomewide molecular markers to predict breeding values and make selections of individuals or breeding lines prior to phenotyping. Here we show that genotyping-by-sequencing (GBS) can be used for de novo genotyping of breeding panels and to develop accurate GS models, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS we discovered 41,371 single nucleotide polymorphisms (SNPs) in a set of 254 advanced breeding lines from CIMMYT’s semiarid wheat breeding program. Four different methods were evaluated for imputing missing marker scores in this set of unmapped markers, including random forest regression and a newly developed multivariate-normal expectation-maximization algorithm, which gave more accurate imputation than heterozygous or mean imputation at the marker level, although no significant differences were observed in the accuracy of genomic-estimated breeding values (GEBVs) among imputation methods. Genomic-estimated breeding value prediction accuracies with GBS were 0.28 to 0.45 for grain yield, an improvement of 0.1 to 0.2 over an established marker platform for wheat. Genotyping-by-sequencing combines marker discovery and genotyping of large populations, making it an excellent marker platform for breeding applications even in the absence of a reference genome sequence or previous polymorphism discovery. In addition, the flexibility and low cost of GBS make this an ideal approach for genomics-assisted breeding.

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