title: Selfing for the design of genomic selection experiments in biparental plant populations.
abstract: Self-fertilization (selfing) is commonly used for population development in plant breeding, and it is well established that selfing increases genetic variance between lines, thus increasing response to phenotypic selection. Furthermore, numerous studies have explored how selfing can be deployed to maximal benefit in the context of traditional plant breeding programs (Cornish in Heredity 65:201-211,1990a, Heredity 65:213-220,1990b; Liu et al. in Theor Appl Genet 109:370-376, 2004; Pooni and Jinks in Heredity 54:255-260, 1985). However, the impact of selfing on response to genomic selection has not been explored. In the current study we examined how selfing impacts the two key aspects of genomic selection-GEBV prediction (training) and selection response. We reach the following conclusions: (1) On average, selfing increases genomic selection gains by more than 70 %. (2) The gains in genomic selection response attributable to selfing hold over a wide range population sizes (100-500), heritabilities (0.2-0.8), and selection intensities (0.01-0.1). However, the benefits of selfing are dramatically reduced as the number of QTLs drops below 20. (3) The major cause of the improved response to genomic selection with selfing is through an increase in the occurrence of superior genotypes and not through improved GEBV predictions. While performance of the training population improves with selfing (especially with low heritability and small population sizes), the magnitude of these improvements is relatively small compared with improvements observed in the selection population. To illustrate the value of these insights, we propose a practical genomic selection scheme that substantially shortens the number of generations required to fully capture the benefits of selfing. Specifically, we provide simulation evidence that indicates the proposed scheme matches or exceeds the selection gains observed in advanced populations (i.e. F 8 and doubled haploid) across a broad range of heritability and QTL models. Without sacrificing selection gains, we also predict that fully inbred candidates for potential commercialization can be identified as early as the F 4 generation.
authors: Nature Source Genetics, 33 Thornwood Drive Suite 300, Ithaca, NY, 14850, USA, bmcclosky@naturesourcegenetics.com.
authors: Benjamin
authors: B
authors: McClosky
authors: Jason
authors: J
authors: LaCombe
authors: Steven D
authors: SD
authors: Tanksley
mesh_terms: D001947:Breeding; D003198:Computer Simulation; D003433:Crosses, Genetic; D005306:Fertilization / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D006579:Heterozygote; D008957:Models, Genetic; D010944:Plants / Q000235:genetics*; D012641:Selection, Genetic
references: PLoS Genet. 2010 May 06;6(5):e1000940
references: 20463887
references: PLoS Genet. 2008 Oct;4(10):e1000231
references: 18949033
references: Genetics. 2004 Dec;168(4):2141-55
references: 15611182
references: Genetics. 2000 Dec;156(4):2093-107
references: 11102398
references: Genetics. 2008 Sep;180(1):611-8
references: 18757934
references: Genetics. 2009 Nov;183(3):1119-26
references: 19704013
references: Genetics. 2001 Apr;157(4):1819-29
references: 11290733
references: Science. 2009 Aug 7;325(5941):714-8
references: 19661422
references: Heredity (Edinb). 1990 Oct;65 ( Pt 2):201-11
references: 2272849
references: J Anim Breed Genet. 2006 Aug;123(4):218-23
references: 16882088
references: BMC Proc. 2010 Mar 31;4(Suppl 1 Proceedings of the 13th European workshop on QTL map):S5
references: 20380759
references: Genetics. 2009 May;182(1):355-64
references: 19299342
references: Theor Appl Genet. 2011 Jul;123(2):339-50
references: 21505832
references: Genetics. 2010 Jul;185(3):1021-31
references: 20407128
references: Theor Appl Genet. 2008 Apr;116(6):815-24
references: 18219476
references: Genet Res (Camb). 2009 Oct;91(5):307-11
references: 19922694
references: Theor Appl Genet. 2004 Jul;109(2):370-6
references: 15069599
references: PLoS One. 2008;3(10):e3395
references: 18852893
references: Theor Appl Genet. 1993 Oct;87(1-2):278-87
references: 24190225
references: Theor Appl Genet. 1989 Sep;78(3):365-8
references: 24227243
references: Theor Appl Genet. 2009 Dec;120(1):151-61
references: 19841887
references: Theor Appl Genet. 1993 Jan;85(5):625-31
references: 24195938
references: Heredity (Edinb). 1990 Oct;65 ( Pt 2):213-20
references: 2272850
references: Theor Appl Genet. 2012 Feb;124(2):261-75
references: 21938474
references: J Anim Breed Genet. 2007 Dec;124(6):323-30
references: 18076469
references: Theor Appl Genet. 2007 Sep;115(5):665-74
references: 17673971
references: Science. 2009 Aug 7;325(5941):737-40
references: 19661427
references: Theor Appl Genet. 1977 May;49(3):111-5
references: 24407167
references: Theor Appl Genet. 1982 Sep;61(3):215-8
references: 24270431