Little heterosis found in diploid hybrid potato: The genetic underpinnings of a new hybrid crop.

Hybrid potato breeding has become a novel alternative to conventional potato breeding allowing breeders to overcome intractable barriers (e.g. tetrasomic inheritance, masked deleterious alleles, obligate clonal propagation) with the benefit of seed-based propagule, flexible population design, and the potential of hybrid vigor. Until now, however, no formal inquiry has adequately examined the relevant genetic components for complex traits in hybrid potato populations. In this present study, we use a 2-step multivariate modeling approach to estimate the variance components to assess the magnitude of the general and specific combining abilities in diploid hybrid potato. Specific combining ability effects were identified for all yield components studied here warranting evidence of nonadditive genetic effects in hybrid potato yield. However, the estimated general combining ability effects were on average 2 times larger than their respective specific combining ability quantile across all yield phenotypes. Tuber number general combining abilities and specific combining abilities were found to be highly correlated with total yield's genetic components. Tuber volume was shown to have the largest proportion of additive and nonadditive genetic variation suggesting under-selection of this phenotype in this population. The prominence of additive effects found for all traits presents evidence that the mid-parent value alone is useful for hybrid potato evaluation. Heterotic vigor stands to be useful in bolstering simpler traits but this will be dependent on target phenotypes and market requirements. This study represents the first diallel analysis of its kind in diploid potato using material derived from a commercial hybrid breeding program.

Neofunctionalisation of the Sli gene leads to self-compatibility and facilitates precision breeding in potato.

Genetic gain in potato is hampered by the heterozygous tetraploid genome of cultivated potato. Converting potato into a diploid inbred-line based F1-hybrid crop provides a promising route towards increased genetic gain. The introduction of a dominant S-locus inhibitor (Sli) gene into diploid potato germplasm allows efficient generation of self-fertilized seeds and thus the development of potato inbred lines. Little is known about the structure and function of the Sli locus. Here we describe the mapping of Sli to a 12.6 kb interval on chromosome 12 using a recombinant screen approach. One of two candidate genes present in this interval shows a unique sequence that is exclusively present in self-compatible lines. We describe an expression vector that converts self-incompatible genotypes into self-compatible and a CRISPR-Cas9 vector that converts SC genotypes into SI. The Sli gene encodes an F-box protein that is specifically expressed in pollen from self-compatible plants. A 533 bp insertion in the promotor of that gene leads to a gain of function mutation, which overcomes self-pollen rejection.

Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum).

With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated "DM", has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of Solyntus as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, Solyntus provides a more direct and contiguous reference then ever before available. It was constructed by sequencing with state-of-the-art long and short read technology and assembled with Canu. The 116 contigs were assembled into scaffolds to form each pseudochromosome, with three contigs to 17 contigs per chromosome. This assembly contains 93.7% of the single-copy gene orthologs from the Solanaceae set and has an N50 of 63.7 Mbp. The genome and related files can be found at https://www.plantbreeding.wur.nl/Solyntus/ With the release of this research line and its draft genome we anticipate many exciting developments in (diploid) potato research.