A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines

Abstract

Developing new potato varieties with enhanced resistance to diseases and pests is essential for ensuring food security and promoting sustainable agricultural production. INRAE has been creating potato advanced breeding lines for over 50 years by crossing different wild potato species with Solanum tuberosum to improve various traits, such as resistance to major pests and diseases or quality traits. These breeding lines have been distributed to French potato breeders, contributing significantly to the development of more resilient potato varieties. However, further research progress is needed to breed durable multi-resistant potato varieties adapted to low-input (mainly pesticides and fertilizer) agriculture. Molecular markers can effectively assist in pyramiding multiple loci for resistance (Pilet-Nayel et al., 2017) to major diseases and pests of potato, such as late blight disease, cyst nematodes, and viruses, while preserving the agronomic and quality values of varieties.The development of genomics and the evolution of sequencing methods in the last decade have facilitated the identification of a large number of SNPs (Single Nucleotide polymorphism) from sequencing data. SNPs discovered using EST (Expressed Sequence Tag) or transcriptome data from six potato varieties were used to construct the widely used Infinium 8K SNP SolCAP array (Hamilton et al., 2011; Felcher et al., 2012). However, this genotyping method may display ascertainment bias especially for germplasm containing Frontiers in Plant Science frontiersin.org 01