Strategies of preserving genetic diversity while maximizing genetic response from implementing genomic selection in pulse breeding programs

Abstract

Genomic selection maximizes genetic gain by recycling parents to germplasm pool earlier and preserves genetic diversity by restricting the number of fixed alleles and the relationship in pulse breeding programs. Using a stochastic computer simulation, we investigated the benefit of optimization strategies in the context of genomic selection (GS) for pulse breeding programs. We simulated GS for moderately complex to highly complex traits such as disease resistance, grain weight and grain yield in multiple environments with a high level of genotype-by-environment interaction for grain yield. GS led to higher genetic gain per unit of time and higher genetic diversity loss than phenotypic selection by shortening the breeding cycle time. The genetic gain obtained from selecting the segregating parents early in the breeding cycle (at F₁ or F₂ stages) was substantially higher than selecting at later stages even though prediction accuracy was moderate. Increasing the number of F₁ intercross (F_1i) families and keeping the total number of progeny of F_1i families constant, we observed a decrease in genetic gain and increase in genetic diversity, whereas increasing the number of progeny per F_1i family while keeping a constant number of F_1i families increased the rate of genetic gain and had higher genetic diversity loss per unit of time. Adding 50 F₂ family phenotypes to the training population increased the accuracy of genomic breeding values (GEBVs) and genetic gain per year and decreased the rate of genetic diversity loss. Genetic diversity could be preserved by applying a strategy that restricted both the percentage of alleles fixed and the average relationship of the group of selected parents to preserve long-term genetic improvement in the pulse breeding program.

Fig. 1

Diagram of simulated pulse breeding programs for phenotypic selection and genomic selection. $\mathrm{\nabla }$: selection on phenotypic selection, ∆: selection on the genomic breeding values, SSD: single seed descent, and aSSD: accelerated single seed descent

Fig. 2

Mean annual aggregated genetic gain (a), TBV variance (b), percentage of alleles fixed (c) and the genomic relationship (d) achieved with parents selected from Stage 2 (STG2) with PS and STG2, F₆, F₂ or F₁ with GS single-seed-descent (SSD) or accelerated SSD (aSSD)

Fig. 3

The accuracy of GEBVs for disease resistance, grain weight and grain yield in GS with single-seed-descend (SSD) in F₃-F₆ when parents were selected from Stage 2 (STG2), F₆, F₂ or F₁

Fig. 4

Mean annual aggregated genetic gain and the genomic relationship in GS with parents selected from Stage 2 (STG2), F₆ or F₂ for scenarios with 100, 200 and 400 F_1i families to make a constant number of 4000  seeds

Fig. 5

Mean annual aggregated genetic gain and the genomic relationship in GS with parents selected from Stage 2 (STG2), F₆ or F₂ for scenarios with different number of 20, 40 or 80 seeds per F_1i family to make 4000, 8000 or 16,000 seeds in total from a constant 200 F_1i families

Fig. 6

Mean annual changes of genetic gain (a) and TBV variance (b) in disease resistance, grain weight and grain yield, percentage of alleles fixed (c) and the genomic relationship (d) between scenarios with (grey bars, GS_aSSD_F₂_PH) or without (white bars, GS_aSSD_F₂) additional phenotypes from F₂ families in GS with aSSD in F₃–F₆ when parents were selected from F₂

Fig. 7

The accuracy of GEBVs for disease resistance, grain weight and grain yield in genomic selection with (GS_aSSD_F₂_PH) or without (GS_aSSD_F₂) adding additional phenotypes from F₂ families in GS with aSSD in F₃–F₆ when parents were selected from F₂

Fig. 8

Mean annual changes of the aggregated genetic gain (a) and the aggregated TBV variance (b), percentage of alleles fixed (c) and the genomic relationship (d) between scenarios with (grey bars) or without (white bars) genetic diversity preservation strategy in GS with aSSD in F₃–F₆ when parents were selected from Stage 2 (STG2) and F₂. Scenario with preservation strategy had a penalty on the genomic relationship (${\lambda }_1$=1) and a penalty on the number of alleles fixed (${\lambda }_2$=10^–6)