Converting Hybrid Potato Breeding Science into Practice

Jan and mini-Jan, a model system for potato functional genomics

Potato (Solanum tuberosum) is the third most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags relative to other major food crops due primarily to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan', which possesses all essential characteristics for facile functional genomics studies. Jan has a high level of homozygosity after seven generations of self-pollination. Jan is vigorous and highly fertile with outstanding tuber traits, high regeneration rates, and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated genes, and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two "mini-Jan" lines with compact and dwarf plant stature using CRISPR/Cas9-mediated mutagenesis targeting the Dwarf and Erecta genes related to growth. Mini-Jan mutants are fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan provide an outstanding model system that can be leveraged for gene editing and functional genomics research in potato.

Quantifying differences in plant architectural development between hybrid potato (Solanum tuberosum) plants grown from two types of propagules

BACKGROUND AND AIMS

Plants can propagate generatively and vegetatively. The type of propagation and the resulting propagule can influence the growth of the plants, such as plant architectural development and pattern of biomass allocation. Potato is a species that can reproduce through both types of propagation: through true botanical seeds and seed tubers. The consequences of propagule type on the plant architectural development and biomass partitioning in potatoes are not well known. We quantified architectural differences between plants grown from these two types of propagules from the same genotype, explicitly analysing branching dynamics above and below ground, and related these differences to biomass allocation patterns.

METHODS

A greenhouse experiment was conducted, using potato plants of the same genotype but grown from two types of propagules: true seeds and seed tubers from a plant grown from true seed (seedling tuber). Architectural traits and biomass allocation to different organs were quantified at four developmental stages. Differences between true-seed-grown and seedling-tuber-grown plants were compared at the whole-plant level and at the level of individual stems and branches, including their number, size and location on the plant.

KEY RESULTS

A more branched and compact architecture was produced in true-seed-grown plants compared with seedling-tuber-grown plants. The architectural differences between plants grown from true seeds and seedling tubers appeared gradually and were attributed mainly to the divergent temporal-spatial distribution of lateral branches above and below ground on the main axis. The continual production of branches in true-seed-grown plants indicated their indeterminate growth habit, which was also reflected in a slower shift of biomass allocation from above- to below-ground branches, whereas the opposite trend was found in seedling-tuber-grown plants.

CONCLUSIONS

In true-seed-grown plants, lateral branching was stronger and determined whole-plant architecture and plant function with regard to light interception and biomass production, compared with seedling-tuber-grown plants. This different role of branching indicates that a difference in preference between clonal and sexual reproduction might exist. The divergent branching behaviours in true-seed-grown and seedling-tuber-grown plants might be regulated by the different intensity of apical dominance, which suggests that the control of branching can depend on the propagule type.

Reproducible Quantitative Trait Loci for Resistance to Soft Rot Caused by Dickeya dianthicola Derived from the Wild Potato Solanum microdontum (PI 458355) Are Located on Chromosomes 1, 3, and 5

The potato wild relative Solanum microdontum is a breeder-friendly source of genetic resistance to soft rot. Our objectives were to (i) identify loci associated with soft rot resistance in S. microdontum germplasm and (ii) develop bi-parental populations in a self-compatible S. tuberosum genetic background to recover segregating F2 progenies, construct a linkage map, and identify quantitative trait loci (QTLs). Under objective (i), tubers from 103 S. microdontum genotypes from the United States Potato Genebank were inoculated with a high virulence strain of Dickeya dianthicola, and lesion size was measured after a 24-h incubation period at 30°C. Association analysis using 3,490 polymorphic Infinium array SNP markers identified soft rot resistance loci on chromosomes 1, 2, 3, 5, 7, 8, 11, and 12. Under objective (ii), a resistant S. microdontum accession PI 458355 was crossed with a highly fertile, self-compatible, diploid S. tuberosum pollen parent (PI 654351) to generate segregating F2 populations. Composite interval mapping was conducted using a genetic linkage map with 970 GBS-based SNP markers. Reproducible QTLs were detected on chromosomes 1, 3, and 5, explaining 11, 13, and 23% of the phenotypic variation, respectively. Homozygous S. microdontum alleles at the QTL on chromosome 5 and heterozygous or homozygous S. microdontum alleles at QTLs on chromosomes 1 and 3 significantly decrease lesion size compared with the homozygous S. tuberosum parent. The germplasm created in these studies provides a resource for studying traits from S. microdontum, and we can use the advanced F2 selections for future potato improvement. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

Crossover shortage in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility

The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers (COs). A strong reduction of CO number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation of univalents during meiosis I and ultimately to the production of unbalanced and sterile gametes. However, if CO shortage is combined with another meiotic alteration that restitutes the first meiotic division, then uniform and balanced unreduced male gametes, essentially composed of nonrecombinant homologs, are produced. This mitosis-like division is of interest to breeders because it transmits most of the parental heterozygosity to the gametes. In potato, CO shortage, a recessive trait previously referred to as desynapsis, was tentatively mapped to chromosome 8. In this article, we have fine-mapped the position of the CO shortage locus and identified StMSH4, an essential component of the class I CO pathway, as the most likely candidate gene. A 7 base-pair insertion in the second exon of StMSH4 was found to be associated with CO shortage in our mapping population. We also identified a second allele with a 3,820 base-pair insertion and confirmed that both alleles cannot complement each other. Such nonfunctional alleles appear to be common in potato cultivars. More than half of the varieties we tested are carriers of mutational load at the StMSH4 locus. With this new information, breeders can choose to remove alleles associated with CO shortage from their germplasm to improve fertility or to use them to produce highly uniform unreduced male gametes in alternative breeding schemes.

Challenges for crop improvement

The genetic improvement of crops faces the significant challenge of feeding an ever-increasing population amidst a changing climate, and when governments are adopting a 'more with less' approach to reduce input use. Plant breeding has the potential to contribute to the United Nations Agenda 2030 by addressing various sustainable development goals (SDGs), with its most profound impact expected on SDG2 Zero Hunger. To expedite the time-consuming crossbreeding process, a genomic-led approach for predicting breeding values, targeted mutagenesis through gene editing, high-throughput phenomics for trait evaluation, enviromics for including characterization of the testing environments, machine learning for effective management of large datasets, and speed breeding techniques promoting early flowering and seed production are being incorporated into the plant breeding toolbox. These advancements are poised to enhance genetic gains through selection in the cultigen pools of various crops. Consequently, these knowledge-based breeding methods are pursued for trait introgression, population improvement, and cultivar development. This article uses the potato crop as an example to showcase the progress being made in both genomic-led approaches and gene editing for accelerating the delivery of genetic gains through the utilization of genetically enhanced elite germplasm. It also further underscores that access to technological advances in plant breeding may be influenced by regulations and intellectual property rights.

Responsible Innovation in Plant Breeding: The Case of Hybrid Potato Breeding

As an emerging innovation, hybrid potato breeding raises high expectations about faster variety development and clean true potato seed as a new source of planting material. Hybrid breeding could, therefore, substantially contribute to global food security and other major sustainable development goals. However, its success will not only depend on the performance of hybrid potato in the field, but also on a range of complex and dynamic system conditions. This article is based on a multidisciplinary project in which we have studied the innovation dynamics of hybrid potato breeding and explored how these dynamics may shape the future of hybrid potato. Inspired by the approach of responsible innovation, we closely involved key players in the Dutch and international potato sector and other relevant actors in thinking about these potato futures. An important and recurrent theme in our work is the tension between the predominant commercial innovation dynamics in plant breeding and promises to respond to the global challenges of food security, agrobiodiversity and climate change. In this article, we, therefore, discuss responsible innovation strategies in (hybrid) potato breeding, which may help to bridge this tension and finally reflect on the implications for the field of plant breeding in general.