A Two‐Part Strategy for Using Genomic Selection to Develop Inbred Lines

By R. Gaynor, G. Gorjanc, A. Bentley, E. Ober, P. Howell, R. Jackson, I. Mackay, John M. Hickey. 2017

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We propose a strategy for implementing genomic selection in plant breeding programs for developing inbred lines that reorganizes traditional breeding programs into two distinct components. These components are: (i) a population improvement component to develop improved germplasm through rapid recurrent selection and (ii) a product development component to identify new inbred varieties or parents for hybrids using traditional breeding program designs. Stochastic simulations of entire breeding programs over 40 yr were used to evaluate the effectiveness of this strategy relative to a conventional program without genomic selection and programs using three standard strategies of implementing genomic selection. Cost effectiveness was measured by constraining all programs to approximately equal annual operating costs and directly comparing each program’s overall performance. Programs using the two-part strategy generated between 2.36 and 2.47 times more genetic gain than the conventional program and between 1.31 and 1.46 times more genetic gain than the best performing standard genomic selection strategy. These results indicate that the two-part strategy is a cost-effective strategy for implementing genomic selection in plant breeding programs. R.C. Gaynor, G. Gorjanc, and J.M. Hickey, Roslin Institute and Royal (Dick) School of Veterinary Studies, Univ. of Edinburgh, Easter Bush Research Center, Midlothian EH25 9RG, UK; A.R. Bentley, E.S. Ober, P. Howell, R. Jackson, and I.J. Mackay, John Bingham Lab., NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK. Received 5 Sep. 2016. Accepted 25 May 2017. *Corresponding author ( john. hickey@roslin.ed.ac.uk). Assigned to Associate Editor Aaron Lorenz. Abbreviations: 2Part, two-part program with PYT genomic selection; 2Part+H, two-part program with headrow genomic selection; AYT, advanced yield trial; CI, confidence interval; Conv, conventional breeding program; Conv GS, conventional program with genomic selection; EYT, elite yield trial; G ́ Y, genotype-by-year interaction; Head GS, headrow genomic selection program; PYT, preliminary yield trial; PYT GS, preliminary yield trial genomic selection program; QTN, quantitative trait nucleotides; SNP, single nucleotide polymorphism. Published in Crop Sci. 56:2372–2386 (2016). doi: 10.2135/cropsci2016.09.0742 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY license (https:// creativecommons.org/licenses/by/4.0/). Published online August 3, 2017

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/76789328f25614a910eced69a0c76590cd7f22dd

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In Genetics

  1. Ben J. Hayes
  2. Michael E. Goddard
  3. Jean-Luc Jannink
  4. M. Thomson
  5. G. Jiang

In Plant Science

  1. K. Aitken
  2. Ben J. Hayes
  3. M. Thomson
  4. G. Jiang

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