Genome-Wide Association Study of Agronomic and Physiological Traits Related to Drought Tolerance in Potato

Identification by GWAS of marker haplotypes relevant to breed potato for Globodera pallida resistance

KEY MESSAGE

Identified and validated QTL GpaVa_MRQ and GpaIX_MRQ provide robust tools for improving potato resistance to Globodera pallida via marker-assisted selection. Potato (Solanum tuberosum L.), a vital food crop globally, faces significant yield losses due to potato cyst nematodes (PCN). This study aimed to identify and validate genomic regions conferring resistance to Globodera pallida, to facilitate the development of resistant potato varieties through marker-assisted selection (MAS). We conducted Genome-Wide Association Studies (GWAS) on a pre-breeding panel genotyped using Genotyping by Sequencing (GBS) and the SolCAP DNA array. Significant resistance-associated SNP markers were identified on chromosomes III, IV, V, IX and XI. Quantitative trait loci (QTL), including the major-effect QTL GpaVa_MRQ on chromosome V and the QTL GpaIX_MRQ on chromosome IX, were validated and shown to account for substantial phenotypic variance in a validation potato panel. Haplotype-based marker sets were defined at four QTL regions, enabling the practical application of MAS. The successful conversion of SNPs to PACE markers at the two main QTL GpaVa_MRQ and GpaIX_MRQ further supports their use in breeding programs. This study provides valuable insights and robust tools for enhancing potato resistance to G. pallida, contributing to sustainable agricultural practices and global food security.

Variance and covariance components of agronomic and quality traits assessed in tetraploid potato and their implications on practical breeding

Potato is a versatile food crop and major component of human nutrition worldwide. Model calculations and computer simulations can be used to optimize the resource allocation in potato breeding programs but require quantitative genetic parameters. The objectives of our study are to (i) estimate quantitative genetic parameters of the most important phenotypic traits in potato breeding programs, (ii) compare the importance of inter- vs. intra-population variance, (iii) quantify genotypic and phenotypic covariances among phenotypic traits, and (iv) examine the effect of a preselection in the single hills stage on variance and covariance components in later stages of the breeding program. Our study was based on a total of 1066 clones from three breeding programs which were evaluated in a non-orthogonal way in 15 environments for a total of 26 phenotypic traits. The examined traits showed an overall high to medium heritability, and variance analysis revealed trait-specific differences in the influence of the genotypic, environmental, and genotype-environment interaction effect. Accounting for heterogeneity in the residual variances between the 15 environments led to a significant improvement of the variance parameter estimation. The result of our study suggested that the first selection step at the single hills stage did not negatively impact the genetic variability of the target traits implying that the traits assessed in the earlier stages were not correlated with the traits influencing market success. Our results can be used as base for further simulation studies and, thus, help to optimize the resource allocation in breeding programs.

Transcription Factor McHB7 Improves Ice Plant Drought Tolerance through ABA Signaling Pathway

As global climate change continues, drought episodes have become increasingly frequent. Studying plant stress tolerance is urgently needed to ensure food security. The common ice plant is one of the model halophyte plants for plant stress biology research. This study aimed to investigate the functions of a newly discovered transcription factor, Homeobox 7 (HB7), from the ice plant in response to drought stress. An efficient Agrobacterium-mediated transformation method was established in the ice plant, where ectopic McHB7 expression may be sustained for four weeks. The McHB7 overexpression (OE) plants displayed drought tolerance, and the activities of redox enzymes and chlorophyll content in the OE plants were higher than the wild type. Quantitative proteomics revealed 1910 and 495 proteins significantly changed in the OE leaves compared to the wild type under the control and drought conditions, respectively. Most increased proteins were involved in the tricarboxylic acid cycle, photosynthesis, glycolysis, pyruvate metabolism, and oxidative phosphorylation pathways. Some were found to participate in abscisic acid signaling or response. Furthermore, the abscisic acid levels increased in the OE compared with the wild type. McHB7 was revealed to bind to the promoter motifs of Early Responsive to Dehydration genes and abscisic acid-responsive genes, and protein-protein interaction analysis revealed candidate proteins responsive to stresses and hormones (e.g., abscisic acid). To conclude, McHB7 may contribute to enhance plant drought tolerance through abscisic acid signaling.

A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes

High-throughput sequencing-based methods for bulked segregant analysis (BSA) allow for the rapid identification of genetic markers associated with traits of interest. BSA studies have successfully identified qualitative (binary) and quantitative trait loci (QTLs) using QTL mapping. However, most require population structures that fit the models available and a reference genome. Instead, high-throughput short-read sequencing can be combined with BSA of k-mers (BSA-k-mer) to map traits that appear refractory to standard approaches. This method can be applied to any organism and is particularly useful for species with genomes diverged from the closest sequenced genome. It is also instrumental when dealing with highly heterozygous and potentially polyploid genomes without phased haplotype assemblies and for which a single haplotype can control a trait. Finally, it is flexible in terms of population structure. Here, we apply the BSA-k-mer method for the rapid identification of candidate regions related to seed spot and seed size in diploid potato. Using a mixture of F1 and F2 individuals from a cross between 2 highly heterozygous parents, candidate sequences were identified for each trait using the BSA-k-mer approach. Using parental reads, we were able to determine the parental origin of the loci. Finally, we mapped the identified k-mers to a closely related potato genome to validate the method and determine the genomic loci underlying these sequences. The location identified for the seed spot matches with previously identified loci associated with pigmentation in potato. The loci associated with seed size are novel. Both loci are relevant in future breeding toward true seeds in potato.

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.