Gene by gene, wild potato reveals its cold resistance blueprint

Researchers have assembled a high-quality, haplotype-resolved genome of the wild potato species Solanum commersonii, known for its exceptional cold resistance. By integrating long-read sequencing and Hi-C data, the team built two chromosome-level haplotypes and revealed key evolutionary adaptations. They also identified a major genetic locus linked to freezing tolerance through bulked segregant analysis and traditional QTL mapping. This locus, located on chromosome 7 and spanning 1.25 Mb, accounts for 18.81% of the phenotypic variation. The findings provide crucial genetic resources for breeding cold-tolerant potatoes and open the door to cloning key resistance genes.

Cultivated potatoes (Solanum tuberosum) are a global staple but remain vulnerable to frost damage, with growth stalling below 7°C and tissue death below -3°C. In contrast, wild diploid species like S. commersonii can survive freezing conditions as low as -12°C and possess resistance to multiple pathogens. Despite their breeding value, leveraging these traits in cultivated varieties has been limited by genomic complexity and insufficient reference resources. Additionally, the genetic mechanisms behind cold resistance remain poorly understood. Based on these challenges, it is necessary to develop high-quality genome assemblies and conduct in-depth mapping of freezing tolerance loci in wild potato species.

A research team from Huazhong Agricultural University has published a new study (DOI: 10.1093/hr/uhae181) on July 12, 2024, in Horticulture Research, unveiling a chromosome-scale, haplotype-resolved reference genome of the cold-resistant wild potato Solanum commersonii. By combining PacBio HiFi sequencing with Hi-C scaffolding, the researchers not only improved genome assembly quality but also mapped a major QTL for freezing tolerance. The work sets a new benchmark for functional genomics and molecular breeding in potato research.

The team assembled two haplotypes of S. commersonii—CMM5_Hap1 and CMM5_Hap2—measuring 706.48 Mb and 711.55 Mb, respectively, with chromosome anchoring rates above 94%. The contig N50 values exceeded 45 Mb, and BUSCO analysis confirmed over 98% completeness. Comparative genomics revealed expansion in gene families related to hormone metabolism, cell development, and stress responses. Notably, 1,581 genes exhibited signs of positive selection, highlighting evolutionary adaptations to cold and disease.

To map freezing tolerance loci, researchers developed a BC1 population from a cross between S. verrucosum and S. commersonii. Using electrolyte leakage assays at −4°C, they evaluated cold sensitivity in 276 individuals and constructed a genetic linkage map using SSR and indel markers. Bulked segregant analysis (BSA-seq) and traditional QTL mapping converged on a region on chromosome 7, defined between markers SSR179 and Ind88. This 1.25 Mb region contains 88 candidate genes and explains 18.81% of phenotypic variance in cold resistance. Interestingly, false-positive signals on Chr10 and Chr12 were ruled out by marker validation, affirming the precision of the Chr07 locus.

“Our high-quality genome assembly and precise QTL mapping provide essential resources for unraveling the genetic basis of cold tolerance in potatoes,” said Prof. Xingkui Cai, corresponding author of the study. “The identified locus on chromosome 7 is particularly promising for future gene cloning and marker-assisted breeding. This work significantly accelerates the integration of wild resistance traits into cultivated potato lines.”

This research delivers both a genomic framework and a target region for improving cold tolerance in potatoes through molecular breeding. The genome of S. commersonii not only clarifies its evolutionary adaptations but also enables identification of functional genes regulating stress resilience. The mapped QTL on chromosome 7 provides a reliable entry point for future cloning of cold-resistance genes, facilitating the development of cultivars capable of withstanding frost. Ultimately, this work could help stabilize potato yields under climate variability and expand cultivation into cooler regions, contributing to global food security.

###

References

DOI

10.1093/hr/uhae181

Original Source URL

https://doi.org/10.1093/hr/uhae181

Funding information

This project was funded by the National Natural Science Foundation of China (grant number 31871685), the Key-Area Research and Development Program of Guangdong Province (2022B0202060001), the China Agricultural Research System (Potato, CARS-09).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.