Genomic prediction with multiple biparental families.

KEY MESSAGE: For genomic prediction within biparental families using multiple biparental families, combined training sets comprising full-sibs from the same family and half-sib families are recommended to reach high and robust prediction accuracy, whereas inclusion of unrelated families is risky and can have negative effects. In recycling breeding, where elite inbreds are recombined to generate new source material, genomic and phenotypic information from lines of numerous biparental families (BPFs) is commonly available for genomic prediction (GP). For each BPF with a large number of candidates in the prediction set (PS), the training set (TS) can be composed of lines from the same full-sib family or multiple related and unrelated families to increase the TS size. GP was applied to BPFs generated in silico and from two published experiments to evaluate the prediction accuracy ([Formula: see text]) of different TS compositions. We compared [Formula: see text] for individual pairs of BPFs using as TS either full-sib, half-sib, or unrelated BPFs. While full-sibs yielded highly positive [Formula: see text] and half-sibs also mostly positive [Formula: see text] values, unrelated families had often negative [Formula: see text], and including these families in a combined TS reduced [Formula: see text]. By simulations, we demonstrated that optimized TS compositions exist, yielding 5-10% higher [Formula: see text] than the TS including all available BPFs. However, identification of poorly predictive families and finding the optimal TS composition with various quantitative-genetic parameters estimated from available data was not successful. Therefore, we suggest omitting unrelated families and combining in the TS full-sib and few half-sib families produced by specific mating designs, with a medium number (~ 50) of genotypes per family. This helps in balancing high [Formula: see text] in GP with a sufficient effective population size of the entire breeding program for securing high short- and long-term selection progress.

Haploid male fertility and spontaneous chromosome doubling evaluated in a diallel and recurrent selection experiment in maize.

KEY MESSAGE: Mainly additive gene action governed inheritance of haploid male fertility, although epistatic effects were also significant. Recurrent selection for haploid male fertility resulted in substantial improvement in this trait. The doubled haploid (DH) technology offers several advantages in maize breeding compared to the traditional method of recurrent selfing. However, there is still great potential for improving the success rate of DH production. Currently, the majority of haploid plants are infertile after chromosome doubling treatment by antimitotic agents such as colchicine and cannot be selfed for production of DH lines. Improvement in haploid male fertility (HMF) by selection for a higher spontaneous chromosome doubling rate (SDR) has the potential to increase DH production efficiency. To investigate the gene action governing SDR in two breeding populations, we adapted the quantitative-genetic model of Eberhart and Gardner (in Biometrics 22:864-881. https://doi.org/10.2307/2528079 , 1966) for the case of haploid progeny from ten DH lines and corresponding diallel crosses. Furthermore, we carried out three cycles of recurrent selection for SDR in two additional populations to evaluate the selection gain for this trait. Additive genetic effects predominated in both diallel crosses, but epistatic effects were also significant. Entry-mean heritability of SDR observed for haploid progeny of these populations exceeded 0.91, but the single-plant heritability relevant to selection was low, ranging from 0.11 to 0.19. Recurrent selection increased SDR from approximately 5-50%, which suggests the presence of few QTL with large effects. This improvement in HMF is greater than the effect of standard colchicine treatment, which yields at maximum 30% fertile haploids. Altogether, the results show the great potential of spontaneous chromosome doubling to streamline development DH lines and to enable new breeding schemes with more efficient allocation of resources.