title: Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants.
abstract: Heuristic genomic inbreeding controls reduce inbreeding in genomic breeding schemes without reducing genetic gain. Genomic selection is increasingly being implemented in plant breeding programs to accelerate genetic gain of economically important traits. However, it may cause significant loss of genetic diversity when compared with traditional schemes using phenotypic selection. We propose heuristic strategies to control the rate of inbreeding in outbred plants, which can be categorised into three types: controls during mate allocation, during selection, and simultaneous selection and mate allocation. The proposed mate allocation measure GminF allocates two or more parents for mating in mating groups that minimise coancestry using a genomic relationship matrix. Two types of relationship-adjusted genomic breeding values for parent selection candidates ([Formula: see text]) and potential offspring ([Formula: see text]) are devised to control inbreeding during selection and even enabling simultaneous selection and mate allocation. These strategies were tested in a case study using a simulated perennial ryegrass breeding scheme. As compared to the genomic selection scheme without controls, all proposed strategies could significantly decrease inbreeding while achieving comparable genetic gain. In particular, the scenario using [Formula: see text] in simultaneous selection and mate allocation reduced inbreeding to one-third of the original genomic selection scheme. The proposed strategies are readily applicable in any outbred plant breeding program.
authors.affiliation: Agriculture Victoria, Biosciences Research, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, VIC, 3083, Australia. zibei.lin@ecodev.vic.gov.au.|School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC, 3083, Australia. zibei.lin@ecodev.vic.gov.au.
authors.forename: Zibei
authors.identifier: http://orcid.org/0000-0002-7628-0702
authors.initials: Z
authors.lastname: Lin
authors.affiliation: Agriculture Victoria, Biosciences Research, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, VIC, 3083, Australia.
authors.forename: Fan
authors.initials: F
authors.lastname: Shi
authors.affiliation: Agriculture Victoria, Biosciences Research, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, VIC, 3083, Australia.|School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC, 3083, Australia.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Hayes
authors.affiliation: Agriculture Victoria, Biosciences Research, AgriBio, Centre for AgriBioscience, La Trobe University, 5 Ring Road, Bundoora, Melbourne, VIC, 3083, Australia.|School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC, 3083, Australia.
authors.forename: Hans D
authors.initials: HD
authors.lastname: Daetwyler
mesh_terms: D014644:Genetic Variation; D007178:Inbreeding; D008129:Lolium / Q000235:genetics*; D000069600:Plant Breeding / Q000379:methods*; D012641:Selection, Genetic