Selection on Expected Maximum Haploid Breeding Values Can Increase Genetic Gain in Recurrent Genomic Selection

Abstract

Genomic selection (GS) offers the possibility to estimate the effects of genome-wide molecular markers, which can be used to calculate genomic estimated breeding values (GEBVs) for individuals without phenotypes. GEBVs can serve as a selection criterion in recurrent GS, maximizing single-cycle but not necessarily long-term genetic gain. As simple genome-wide sums, GEBVs do not take into account other genomic information, such as the map positions of loci and linkage phases of alleles. Therefore, we herein propose a novel selection criterion called expected maximum haploid breeding value (EMBV). EMBV predicts the expected performance of the best among a limited number of gametes that a candidate contributes to the next generation, if selected. We used simulations to examine the performance of EMBV in comparison with GEBV as well as the recently proposed criterion optimal haploid value (OHV) and weighted GS. We considered different population sizes, numbers of selected candidates, chromosome numbers and levels of dominant gene action. Criterion EMBV outperformed GEBV after about 5 selection cycles, achieved higher long-term genetic gain and maintained higher diversity in the population. The other selection criteria showed the potential to surpass both GEBV and EMBV in advanced cycles of the breeding program, but yielded substantially lower genetic gain in early to intermediate cycles, which makes them unattractive for practical breeding. Moreover, they were largely inferior in scenarios with dominant gene action. Overall, EMBV shows high potential to be a promising alternative selection criterion to GEBV for recurrent genomic selection.

Improving short and long term genetic gain by accounting for within family variance in optimal cross selection

“…Lehermeier et al (2017b) observed that using UC as a cross selection index increased the short 55 term genetic gain compared to evaluate crosses based on OHV or mean parental GEBV. Similar results 56 have been obtained by simulations in Müller et al (2018) considering the expected maximum haploid 57 breeding value (EMBV) that is akin to the UC for normally distributed and fully additive traits. 58…”

“…1A). This tendency was also observed in simulations by Müller et al (2018) considering the EMBV approach, 403 akin to the UC for normally distributed additive traits. The UC also showed a higher long term genetic 404 gain at both commercial (G10) and whole progeny level (G) compared to intercross the best candidate 405 parents (PM).…”

“…7C) of the favorable allele at QTLs compared to PM. These results highlight the interest of 410 considering within cross variance in cross selection for improving long term genetic gain as observed in 411 Müller et al (2018). 412…”

“…Using 42 stochastic simulations, the authors observed that OHV selection yielded higher long term genetic gain 43 and preserved greater amount of genetic diversity than truncated GS. However, OHV does neither 44 account for the position of quantitative trait loci (QTLs) nor the linkage disequilibrium between QTLs 45 (Lehermeier et al 2017b;Müller et al 2018). Schnell and Utz (1975) proposed the usefulness criterion 46 (UC) of a cross to evaluate the expected response to selection in the progeny of the cross.…”

Usefulness Criterion and post-selection Parental Contributions in Multi-parental Crosses: Application to Polygenic Trait Introgression

“…Applying UCPC within 516 the context of mating design optimization would enable to account for parental 517 complementarity through the use of progeny variation, i.e. within cross variance, as proposed 518 by Shepherd and Kinghorn (1998), Akdemir and Sánchez (2016) and Müller et al (2018).…”