Using transcriptome analysis and QTL mapping to decipher the genetic basis of heterosis in potato root system

Heterosis is a crucial theoretical and technological foundation for modern crop improvement, and its utilization has significantly enhanced agricultural productivity. As the most important tuber crop, research on the mechanism of heterosis in potatoes (Solanum tuberosum L.) has just started, especially the research on root heterosis in diploid potato has not been reported yet.

We crossed two diploid materials HD5 and M9 with homozygous genomes to obtain the F₁ hybrid HM with significant root heterosis. Transcriptome sequencing analysis was performed on the roots of 14-day-old hydroponically grown seedlings. A total of 2,156 non-additive expression genes, 5,306 dominant expression genes, 1,345 overdominant expression genes, and 3,246 allele-specific expression genes were obtained. Genetic effect analysis of heterosis showed that the dominant effect was the main mode of action during root development. GO and KEGG enrichment analysis of the above four gene sets indicated that the lignin biosynthesis pathway was involved in regulating the formation of root heterosis. Calculation of heterotic effects for 47 QTLs mapped using the F₂ population showed that overdominance and complete-incomplete dominance constituted the primary heterotic effects of potato roots. Further integration of QTL mapping results with lignin pathway analysis identified six candidate genes related to root development heterosis: DM8C01G33280, DM8C02G28580, DM8C02G29270, DM8C03G31680, DM8C05G27310, and DM8C12G18910.

This study contributes to clarifying the molecular mechanisms of heterosis in potato root development and provides valuable targets for cloning and functional analysis of heterosis-related genes.