Scientists decode frost-resistant pomegranate genome, paving way for hardier fruits
image: Representative phenotypes and genomic features of 'Sanbai'.
Credit: Horticulture Research
A new genomic study provides a breakthrough in understanding cold tolerance in pomegranates, a major hurdle for cultivating prized soft-seeded varieties. Researchers have assembled a high-quality genome of a cold-resistant, hard-seeded pomegranate, 'Sanbai'. This enabled the discovery of widespread structural variations (SVs) driving population differentiation and identified a massive ~5.4-Mb inversion on chromosome 1 strongly linked to cold adaptation. Furthermore, the study pinpointed a key transcription factor, PgNAC12, and demonstrated its role in regulating the PgCBF1 gene to enhance cold stress response. These findings offer crucial genetic insights and valuable resources for breeding cold-tolerant pomegranate varieties, potentially securing the future of the soft-seeded pomegranate industry.
Pomegranate is a globally important fruit tree, valued for its nutritional and health benefits. Consumer preference leans towards soft-seeded varieties due to their superior eating quality. However, these desirable varieties are highly susceptible to cold damage, severely limiting their cultivation and causing significant economic losses. While previous genomic studies identified genes related to seed hardness, the genetic basis of cold tolerance remained poorly understood. This knowledge gap was partly due to the lack of a high-quality reference genome for cold-tolerant, hard-seeded pomegranates and a comprehensive analysis of large-scale genomic differences, particularly structural variations (SVs), across diverse populations. Based on these challenges, a deep investigation into the genomic drivers of cold adaptation was necessary.
In a study published (DOI: 10.1093/hr/uhaf022) on May 1, 2025, in the journal Horticulture Research, a multi-institutional research team from China reported a significant advance in pomegranate genomics. They presented a high-quality, chromosome-level genome assembly for the cold-tolerant 'Sanbai' pomegranate. Utilizing this robust assembly and long-read sequencing data from 38 diverse pomegranate accessions, the team comprehensively cataloged SVs and identified key genomic regions and candidate genes underpinning cold adaptation, marking a critical step forward for the crop's genetic improvement.
The research successfully generated a highly continuous genome for 'Sanbai' (contig N50 of 15.93 Mb), serving as a superior reference. Comparative genomic analysis with a soft-seeded variety revealed over 28,000 SVs. Population genetics using these SVs divided pomegranates into two distinct groups: cold-tolerant, hard-seeded varieties and cold-sensitive, soft-seeded ones. A standout discovery was a ~5.4-Mb inversion on chromosome 1, prevalent in cold-sensitive genotypes, suggesting it acts as a recombination barrier, maintaining haplotypes associated with cold susceptibility.
Through bulk segregant analysis and selective sweep analysis, the researchers identified the PgNAC12 transcription factor as a prime candidate. They found a key amino acid change in PgNAC12 that predominantly exists in cold-sensitive accessions. Functional validation in Arabidopsis confirmed that overexpressing either PgNAC12 or its target gene, PgCBF1, significantly enhanced cold tolerance. Crucially, molecular assays demonstrated that PgNAC12 directly binds to the PgCBF1 promoter to activate its expression, a process intensified under cold stress. This PgNAC12-PgCBF1 regulatory module is a central finding, revealing a molecular mechanism for cold response differentiation.
"This study represents a paradigm shift in pomegranate genomics," said a corresponding author of the study. "The high-quality 'Sanbai' genome, the extensive catalog of SVs, and the functional validation of the PgNAC12-PgCBF1 pathway provide an unprecedented resource. It not only deciphers the genetic architecture of cold tolerance but also offers tangible molecular tools for breeders to develop new, resilient pomegranate cultivars that can thrive in colder environments."
The implications of this research are profound for pomegranate breeding. The identified genetic markers, particularly the large inversion and the PgNAC12 haplotype, can be directly used for marker-assisted selection. This allows breeders to efficiently screen seedling populations for superior cold tolerance traits early on, drastically accelerating the development of new varieties. By integrating these findings, the cultivation of high-value soft-seeded pomegranates could be expanded into regions previously considered too cold, stabilizing production and meeting growing market demand. This genomic resource also opens new avenues for studying other agronomically important traits in pomegranates.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf022
Funding information
This work was supported by the National Natural Science Foundation of China (31901343), Natural Science Foundation of Henan Province (232300420011, 242300420155), Key Research and Development Program of Shandong Providence in China (2022TZXD009), and Shandong Province Agricultural Improved Seed Project (2021LZGC007).
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.