UC Davis

Potatoes (Solanum tuberosum L.) rank among the world's leading staple crops due to their high demand and nutritional value. They are autotetraploid with tetrasomic inheritance, and exhibit high heterozygosity, posing challenges for genetic studies and crop improvement efforts. Moreover, the limited genetic diversity in modern cultivated potatoes makes them vulnerable to diseases and restricts opportunities for increasing productivity. In contrast, wild relatives and landraces display superior phenotypes for many valuable traits and could provide genetic variation absent in cultivated varieties. A method for efficient transfer of these traits to the cultivated pool could help alleviate these limitations. Unfortunately, interspecific hybridization is often hindered by crossing barriers. A promising alternative for harnessing the diversity of potato relatives is through the haploid induction system and its byproducts. In potatoes, haploid induction occurs between tetraploid cultivars and specific diploid lines acting as haploid inducers (HIs). The resulting products from this cross include not only the desired dihaploids, but also triploids, tetraploids, and aneuploids, originating from both the 4x parent and the haploid inducer. Despite their crucial role in the production of dihaploids, haploid inducers (HIs) have not seen significant improvements from a breeding standpoint. Potato breeders prefer HIs that flower profusely and yield many dihaploids. They dislike HIs that generate more instances of extrachromosomal DNA—specifically additional and/or rearrangement HI chromosomes— in the dihaploids. In this study, we compare the haploid induction rate (HIR) of two well-known IvP HIs alongside a new haploid inducer named PL-4, conducting haploid induction crosses using forty elite 4x breeding lines as pistillate parents. Our findings highlight PL-4 as a superior HI, exhibiting an overall higher HIR (11.6%) compared to IvP101 and IvP35 (6.8% and 4.3%, respectively). Additionally, PL-4 demonstrates broad pistillate parent compatibility, irrespective of their cytoplasm type. This suggests that PL-4 can be a valuable asset in a large-scale dihaploid production scheme. As diploid potato breeding advances, the need to understand the diverse karyotypic variations resulting from haploid induction crosses becomes increasingly crucial. While genome instability has been observed among the products of haploid induction in Arabidopsis thaliana, the associated instability in potatoes remains relatively unexplored. The progeny of potato haploid induction may serve as a reservoir for novel rearrangements, including extrachromosomal DNA. The characterization of these novel chromosomal elements could provide tools for precision genome engineering by serving as platforms to introduce new traits and enhance the overall potato genetic landscape. To comprehensively assess the byproducts of haploid induction, our examination began with a thorough analysis of various seed types, followed by detailed phenotypic assessment. We employed IvP48, a HI previously known for harboring residual HI DNA in the resulting progeny. To minimize bias towards well-developed seeds, all seed types underwent in vitro germination. Noteworthy among our findings is the characterization of a new type—shriveled seeds—which encompasses seeds with compromised or partially collapsed endosperm, in addition to the more commonly observed spotted and spotless seeds in this cross. This novel category exhibits an enrichment of aneuploidy types. In summary, our analysis of the dihaploid lines unveiled 15% maternal aneuploidy, with chromosome 8 displaying the most frequent variation in dosage. This observed pattern is attributed to a previously identified translocation between chromosome 7 and chromosome 8 in the Red Polenta cultivar used as the pistillate parent. Similarly to what is observed in the progeny of haploid induction crosses in Arabidopsis thaliana, there is a potential chromothriptic case among the dihaploids that requires further investigation.

Minichromosomes (minis), stand out as the most intriguing byproducts of haploid induction, yet their potential in potato research remains largely unexplored. Remarkably, minis in potato have yet to receive comprehensive study. To help fill this gap, we investigated an A. thaliana line harboring a minichromosome, named mini1a, presenting the first comprehensive characterization of minis resulting from Arabidopsis haploid induction crosses. Our investigation of mini1a has revealed distinctive characteristics, including a meiotic transmission rate of approximately 28% and a confirmed circular structure through cytological examination. Subsequent sequencing revealed the formation of mini-subtypes, showcasing structural variations, particularly in the centromeric regions. Notably, in certain instances, mini1a led to detrimental effects on fertility. The assessment of mini1a's mitotic stability, utilizing a visual trait, yielded inconclusive results, which we attributed to potential silencing of the mini genes. However, a more detailed characterization is still required. Our findings highlight challenges in utilizing minis as vectors for chromosome engineering. Despite their promising potential, successful implementation may encounter obstacles, as evidenced in our study.

In conclusion, this dissertation advances our comprehension of crucial elements in haploid induction, unraveling novel insights for both potato and Arabidopsis. The identification of a new haploid inducer and the exploration of unique chromosome rearrangements, particularly minichromosomes, emerge as pivotal contributions. These findings not only expand our knowledge but may also open avenues for harnessing these novel elements as powerful tools in crop improvement.