Improvement of diagnostic markers for resistance to Globodera pallida and application for selection of resistant germplasms in potato breeding

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.

Polyploid QTL-seq identified QTLs controlling potato flesh color and tuber starch phosphorus content in a plexity-dependent manner

The progenies of polyploid crops inherit multiple sets of homoeologous chromosomes through various combinations, which impedes the identification of the quantitative trait loci (QTL) governing agronomic traits and the implementation of DNA marker-assisted breeding. Previously, we developed a whole-genome sequencing-based polyploid QTL-seq method that utilizes comprehensively extracted simplex polymorphisms for QTL mapping. Here, we verified the detection of duplex QTLs by modifying the analytical settings to explore the QTLs governing tuber flesh color and starch phosphorus content using tetraploid potato (Solanum tuberosum L.). The F1 progenies were obtained from a cross between 'Touya' (TY) and 'Benimaru' (BM). A single TY-derived QTL responsible for yellow flesh color was identified around a β-carotene hydroxylase gene on chromosome 3 using simplex polymorphisms, and a BM-derived QTL associated with decreased starch phosphorus content near a starch synthase II gene on chromosome 2 was detected using duplex polymorphisms. Furthermore, linked DNA markers were developed at the QTL sites. For the latter QTL, plexity-distinguishable markers were developed using quantitative PCR, fragment analysis, and amplicon sequencing. These revealed the allele dosage-dependent effect of the reduced starch phosphorus content. Thus, the polyploid QTL-seq pipeline can explore versatile QTLs beyond simplex, facilitating DNA marker-assisted breeding in various polyploid crops.

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.

Studies of potato resistance to Globodera rostochiensis revealed novel alleles for 57R marker

Globodera rostochiensis resistance has been an important trait in potato (Solanum tuberosum) breeding for decades. Our aim was to complement phenotypic testing with genetic marker analysis. We analysed the results of G. rostochiensis resistance greenhouse testing in 4601 tubers of 2918 breeding clones from 11 years. Applicability of H1 gene markers TG689 and 57R was compared. We implemented the latter with the positive predictive value of 99.1% and negative predictive value of 60.0% into the breeding scheme. The 57R marker alleles of 22 Estonian cultivars and 470 breeding clones were determined. Two unique 57R alleles, 57R-887 and 57R-1155, were found in Estonian cultivar 'Anti'. The 887 bp allele has two deletions (14 bp and 490 bp) accompanied by several other indels and SNPs within the 57R marker region. The 1155 bp allele has three deletions (7 bp, 20 bp and 210 bp) accompanied by several other indels and SNPs within the same region. Partial resistance to G. rostochiensis in 'Anti' suggests that the newly described alleles could affect the H1-mediated resistance directly or indirectly.