Drought and Saline Stress Tolerance Induced in Somatic Hybrids of Solanum chacoense and Potato Cultivars by Using Mismatch Repair Deficiency

Global climate change, especially when involving drought and salinity, poses a major challenge to sustainable crop production, causing severe yield losses. The environmental conditions are expected to further aggravate crop production in the future as a result of continuous greenhouse gas emissions, causing further temperature rise and leading to increased evapotranspiration, severe drought, soil salinity, as well as insect and disease threats. These suboptimal growth conditions have negative impact on plant growth, survival, and crop yield. Potato is well known as a crop extremely susceptible to drought, which is primarily attributed to its shallow root system. With potato being the fourth major food crop, increasing potato productivity is thus important for food security and for feeding global population. To maintain a sustainable potato production, it is necessary to develop stress tolerant potato cultivars that cope with the already ongoing climate change. The aim of our study is to analyze the response of potato somatic hybrids to drought and salt stress under in vitro conditions; the somatic hybrids studied are the wild relative Solanum chacoense (+) Solanum tuberosum, with or without mismatch repair deficiency (MMR). Upon this selection of drought and salt tolerant genotypes, somatic hybrids and their parents were phenotyped on a semi-automated platform, and lines tolerant to medium water scarcity (20% compared to 60% soil water capacity) were identified. Although none of the parental species were tolerant to drought, some of the MMR-deficient somatic hybrids showed tolerance to drought and salt as a new trait.

Incomplete Genome Doubling Enables to Consistently Enhance Plant Growth for Maximum Biomass Production by Altering Multiple Transcript Co-Expression Networks in Potato

Polyploidization is an important approach in crop breeding for agronomic trait improvement, especially for biomass production. Cytochimera contains two or more mixed cells with different levels of ploidy, which is considered a failure in whole genome duplication. Using colchicine treatment with diploid (Dip) potato (Solanum chacoense) seedlings, this study generated tetraploid (Tet) and cytochimera (Cyt) lines, which respectively contained complete and partial cells with genome duplication. Compared to the Dip potato, we observed remarkably enhanced plant growth and biomass yields in Tet and Cyt lines. Notably, the Cyt potato straw, which was generated from incomplete genome doubling, was of significantly higher biomass yield than that of the Tet with a distinctively altered cell wall composition. Meanwhile, we observed that one layer of the tetraploid cells (about 30 %) in Cyt plants was sufficient to trigger a gene expression pattern similar to that of Tet, suggesting that the biomass dominance of Cyt may be related to the proportion of different ploidy cells. Further genome-wide analyses of co-expression networks indicated that down-regulation (against Dip) of spliceosomal-related transcripts might lead to differential alternative splicing for specifically improved agronomic traits such as plant growth, biomass yield and lignocellulose composition in Tet and Cyt plants. In addition, this work examined that the genome of Cyt line was relatively stable after years of asexual reproduction. Hence, this study has demonstrated that incomplete genome doubling is a promising strategy to maximize biomass production in potato and beyond.

Allelic variants of the NLR protein Rpi-chc1 differentially recognise members of the Phytophthora infestans PexRD12/31 effector superfamily through the leucine-rich repeat domain

SummaryPhytophthora infestans is a pathogenic oomycete that causes the infamous potato late blight disease. Resistance (R) genes from diverse Solanum species encode intracellular receptors that recognize P. infestans RXLR effector proteins and provide effective defence responses. To deploy these R genes in a durable fashion in agriculture, we need to understand the mechanism of effector recognition and the way the pathogen evades recognition.We cloned sixteen allelic variants of the Rpi-chc1 gene from Solanum chacoense and other Solanum species, and identified the cognate P. infestans RXLR effectors. These tools were used to study receptor-ligand interactions and co-evolution.Functional and non-functional alleles of Rpi-chc1 encode Coiled-Coil-Nucleotide Binding-Leucine-Rich-Repeat (CNL) proteins. Rpi-chc1.1 recognised multiple PexRD12 (AVRchc1.1) proteins while Rpi-chc1.2 recognised multiple PexRD31 (AVRchc1.2) proteins, both from the PexRD12/31 superfamily. Domain swaps between Rpi-chc1.1 and Rpi-chc1.2 revealed that overlapping subdomains in the LRR were responsible for the difference in effector recognition.This study showed that Rpi-chc1.1 and Rpi-chc1.2, evolved to recognize distinct members of the same PexRD12/31 effector family via the LRR domain. The biased distribution of polymorphisms suggests that exchange of LRRs during host-pathogen co-evolution can lead to novel recognition specificities. These insights will help future strategies to breed for durable resistant varieties.

QTL detection in a pedigreed breeding population of diploid potato

Diploid hybrid potato breeding is emerging as an alternative to breeding tetraploid potato clones. The development of diploid breeding varieties involves recent, shallow pedigrees with a limited number of founders. Within this context, alternative QTL detection methodologies should be considered to enable identification of relevant QTLs and characterize the founders of the pedigree. To that end, we are using a dataset of multiple diploid potato $$\hbox {F}_3$$ F 3 families under selection derived by a cross between an inbred Solanum chacoense and an outbred diploid Solanum tuberosum, and identify QTLs for tuber fresh weight. We used three methods for QTL detection: (1) a Genome Wide Association Study model, (2) a linkage approach tailored to the population under study and (3) a more general approach for modelling multiallelic QTLs in complex pedigrees using identity-by-descent (IBD) probabilities. We show that all three approaches enable detection of QTLs in the population under study, but the method that makes better use of IBD information has a more direct and detailed interpretation by linking QTL alleles to the founders.