Lychee’s Genetic Relationships Uncovered Through DNA Markers Revealing Hidden Variety Diversity

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Lychee, a tropical fruit cherished for its sweet flavor and nutritional richness, has been cultivated for over 2,000 years. Despite its long history, lychee remains underutilized globally due to challenges like inconsistent yields, climate sensitivity, and confusion over cultivar identities.

A recent study published in Genetic Resources and Crop Evolution (2025) offers groundbreaking insights into the genetic diversity of lychee, revealing critical information that could transform how this fruit is grown, conserved, and improved.

Understanding Lychee Genetic Diversity Through USDA Research

Researchers analyzed 91 lychee trees from the USDA’s Hawai’i collection, representing 57 named cultivars and 13 unnamed varieties.

The study aimed to answer three critical questions: First, how is genetic variation—differences in DNA sequences among individuals—distributed among lychee cultivars? Second, are trees labeled as the same cultivar truly genetically identical? Third, are there cases where different names refer to the same cultivar or the same name masks genetic differences (homonymy)?

To achieve this, the team used advanced DNA sequencing techniques, focusing on single nucleotide polymorphisms (SNPs)—tiny genetic variations where a single DNA building block (nucleotide) differs between individuals. SNPs act like fingerprints, helping scientists distinguish cultivars and trace their ancestry.

Advanced DNA Sequencing Techniques for Lychee Cultivar Analysis

The process began with collecting leaf samples from each tree.

Scientists extracted DNA using a chemical method called CTAB (cetyltrimethylammonium bromide) protocol, which breaks down plant cell walls to isolate genetic material.

This method is preferred for plants like lychee because it effectively removes compounds that can interfere with DNA analysis. They then used a technique called Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) to examine specific regions of the lychee genome.

SLAF-Seq is a cost-effective method that targets “tags” of DNA cut by restriction enzymes, allowing researchers to focus on variable regions. This method generated over 4 million genetic markers, which were filtered to remove low-quality data, leaving 10,379 reliable SNPs for analysis.

These markers were used to build phylogenetic trees diagrams that show evolutionary relationships and group similar cultivars. Additionally, a gene called COL307, linked to flowering time, was tested using PCR (polymerase chain reaction), a method to amplify specific DNA segments.

• PCR confirmed the presence or absence of a 3.7-kilobase deletion in this gene, which influences when lychee trees flower and fruit.

Key Genetic Groups in Lychee and Their Impact on Harvest Timing

The study confirmed that lychee cultivars fall into two main genetic groups. The first group, called Late-Maturing Cultivars (LMCs), originated in Hainan, China. These trees produce high-quality fruits but require longer growing seasons. Examples include Kwai Mi and Wai Chee.

The second group, Extremely Early-Maturing Cultivars (EEMCs), comes from Yunnan, China. These trees fruit earlier but yield smaller, less desirable fruits, such as Sam Yu Hung. Between these groups lies a mix of hybrids, termed Early-Maturing Cultivars (EMCs), which combine traits from both parent groups.

Nearly half of the USDA collection (41 out of 91 trees) belonged to this admixed category meaning their DNA shows a blend of LMC and EEMC ancestry—reflecting their popularity in global orchards.

A pivotal discovery was the role of the COL307 gene in determining flowering time. Genes are segments of DNA that carry instructions for building proteins, which govern traits like growth and development. LMCs possess the full version of this gene, delaying flowering, while EEMCs have a 3.7-kilobase deletion (a loss of 3,700 DNA base pairs) that triggers early flowering.

Hybrids (EMCs) carry one intact and one deleted copy, leading to intermediate maturity. PCR tests on 42 accessions revealed 21 trees with the full gene (LMCs), 5 with the deletion (EEMCs), and 16 hybrids (EMCs). This finding simplifies breeding efforts, as farmers can now select parents based on genetic markers rather than trial and error.

Uncovering Mislabeled Lychee Cultivars and Their True Identities

One of the study’s most striking revelations was the extent of mislabeling in lychee collections. Genetic analysis identified 13 groups of identical trees, despite different names or “unknown” labels. For example, Hak Ip (Thailand) and O-Hia (Hawaii) were genetically identical, as were No Mai Tsze (China), Salathiel (Australia), and Wai Chee (Thailand).

These findings highlight how historical trade and language barriers led to duplicated cultivars under different names. Synonymous cultivars—genetically identical plants with different names—often arise when a single variety is introduced to new regions and renamed.

Conversely, some cultivars shared names but were genetically distinct, a problem called homonymy. Five trees labeled No Mai Tsze appeared in four separate genetic clusters, indicating severe mislabeling. Similarly, two Kwai Mi Pink accessions were unrelated, suggesting documentation errors.

Among the 13 unnamed trees, most matched existing cultivars. For instance, Unknown 9 was identical to Ito (Japan), while Unknown 11 matched Kai Ju Lai (China). Only two unknowns remained unique, underscoring gaps in the USDA’s records.

12 Essential SNP Markers for Accurate Lychee Cultivar Identification

To address mislabeling, researchers identified 12 SNP markers capable of distinguishing all 91 accessions.

SNPs are the most common type of genetic variation and serve as reliable markers for identification.

These markers, spread across lychee’s 15 chromosomes (thread-like structures that carry DNA), act as a genetic barcode.

For example, a SNP on chromosome 8 (position 6,936,632) differentiates Kwai Mi from Kwai Mi Pink. This core SNP set enables rapid, cost-effective identification using basic PCR tests, replacing time-consuming morphological checks. Farmers and breeders can now verify sapling identities with precision, reducing errors in orchards and nurseries.

Enhancing Lychee Germplasm Conservation & Sustainable Farming Practices

The USDA’s lychee collection includes 94 accessions, but 60% (55 trees) were genetic duplicates. Germplasm collections—repositories of genetic material like seeds or live plants—aim to preserve biodiversity, but duplicates waste resources.

• Removing clones could free space to conserve unique varieties, such as Kaimana (a Hawaiian hybrid) or Brewster (mislabeled as Chan Tsee).

Conservation efforts are critical, as lychee’s wild relatives harbor traits like drought tolerance—the ability to survive with limited water—that could bolster commercial varieties.

For farmers, genetically verified cultivars promise higher yields. In Thailand and Vietnam, average lychee production is 2–3.5 tonnes per hectare, far below China’s 15 tonnes. Improved cultivars could close this gap by resisting pests like lychee crinose mites, tiny insects that damage flowers and reduce yields.

Better orchard management—such as avoiding overcrowded trees—could further enhance productivity. Cultivar selection, choosing plants best suited to local conditions, is key to maximizing harvests.

Addressing Climate Challenges and Promoting Global Lychee Collaboration

Climate change poses a significant threat to lychee cultivation. The trees require cool periods (below 20°C) to trigger flowering, but rising temperatures disrupt this cycle. Solutions include gene editing—a technology like CRISPR to modify DNA—to alter COL307 or crossbreeding with wild relatives for drought resilience (ability to thrive in dry conditions).

Expanding genetic research is equally vital. While this study analyzed 91 accessions, China’s National Lychee Germplasm Resources hold over 400 cultivars. Sequencing these could uncover traits like disease resistance or longer shelf life, reducing post-harvest losses.

Global collaboration is another priority. Historical renaming—such as Tai So becoming Mauritius—complicates international trade. A unified naming system, backed by genetic data and managed by groups like the FAO (Food and Agriculture Organization), could streamline efforts.

Such initiatives would empower farmers, breeders, and policymakers to work toward a common goal: making lychee a staple crop—a primary food source for populations.

Conclusion

This study marks a turning point for lychee. By decoding its genetic diversity—the variety of DNA within a species—scientists have provided tools to combat mislabeling, enhance breeding, and conserve rare varieties. For farmers, this means access to reliable, high-yielding cultivars. For consumers, it promises a steadier supply of nutritious lychee fruits. As climate change and population growth intensify, such research isn’t just about improving a fruit—it’s about securing a sustainable future for global agriculture.

Lychee’s journey from ancient Chinese courts to modern supermarkets is a testament to its enduring appeal. With genetics as a guide, this fruit is poised to step out of obscurity and become a cornerstone of 21st-century food systems. By embracing science and collaboration, we can ensure lychee thrives for generations to come.