Scientists develop litchi40K: A cost-effective genotyping tool for faster litchi breeding
image: Population structure in the L. chinensis var. fulvosus population with Litchi40K v1.0. A. The genome-wide SNP identified in the L. chinensis var. fulvosus population. B. PCA plot of the L. chinensis var. fulvosus population. C. The phylogenetic analysis and ancestral component analysis from K values 2 to 5 of the L. chinensis var. fulvosus population. D. Spatial population structure with K = 2. E. Spatial population structure with K = 3. Image link: https://academic.oup.com/view-large/figure/511947305/uhaf038f2.tif?login=false
Credit: Horticulture Research
Litchi is an important subtropical fruit crop widely cultivated across China and Southeast Asia, yet its breeding progress is constrained by limited varietal diversity, long juvenile growth cycles, and inconsistent trait inheritance. Traditional germplasm classification is further complicated by regional synonym issues and ambiguous parentage in breeding populations. Although molecular markers have been used to distinguish flowering and maturation traits, current genotyping approaches often face high cost, low resolution in heterozygous sites, or insufficient flexibility for large-scale breeding applications. Due to these challenges, there is a need to develop an efficient, accurate, and scalable genotyping platform to support trait-associated allele discovery and germplasm digitalization.
Researchers from the Chinese Academy of Tropical Agricultural Sciences and collaborating institutions reported a breakthrough in genotyping technology for litchi. The study, published (DOI: 10.1093/hr/uhaf038) in Horticulture Research on February 10, 2025, introduces Litchi40K v1.0, a liquid SNP chip designed from resequencing data of 875 accessions. This platform was validated across diverse applications, including population genetics, trait association, genetic mapping, and germplasm identity verification, significantly improving the precision and efficiency of litchi breeding.
Litchi40K v1.0 contains 40,230 curated SNP markers distributed evenly across the genome and optimized for high polymorphic information content. When applied to L. chinensis var. fulvosus, the chip successfully resolved three subpopulation groups and identified 1,110 candidate genes under differentiation, including LITCHI012464, a lysine demethylase potentially linked to adaptation to solar radiation. Genome-wide association analysis revealed 30 genomic regions associated with key fruit and leaf traits. Notably, a haplotype (H002) of LITCHI026966, encoding a glucan endo-1,3-β-glucosidase, was found to significantly increase soluble solid content and predominates within the Sub2 subgroup.
In a biparental F1 hybrid population, the chip enabled construction of a high-density genetic map and identification of 79 QTLs associated with dwarfing traits. Within a major stable QTL on chromosome 10, LITCHI022305, an NAC transcription factor, was identified as a candidate gene containing a frameshift variant likely contributing to growth reduction.
To support resource digitalization, the authors derived a compact fingerprint panel (Litchi384 v1.0), enabling cultivar identity verification, pedigree tracing, and detection of synonym and bud-mutation groups.
"Our goal was to create a genotyping system that is not only scientifically robust but also practical for breeders," the authors explained. "The Litchi40K v1.0 chip integrates high-resolution genomic data with flexible application potential, allowing breeders to identify useful alleles, accelerate hybrid selection, and standardize germplasm identification. As litchi breeding enters the genomics era, tools like this will help bridge the gap between molecular research and field application."
Litchi40K v1.0 and its derivative fingerprint system provide a foundation for modernizing litchi breeding strategies. By enabling early screening of superior seedlings, identifying elite haplotypes, and clarifying genetic relationships among varieties, the platform reduces breeding time, enhances cultivar authenticity, and supports the development of improved varieties with better fruit quality and adaptive traits. The low cost and upgradability of the liquid chip also make it suitable for large-scale breeding programs and long-term germplasm management. This work positions litchi breeding to adopt genomic selection approaches widely used in major crops.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf038
Funding information
This paper was supported by the funds of Science and Technology Special Fund of Hainan Province (ZDYF2023XDNY080), National Key R&D Program of China (2021YFD1200204), the earmarked fund for CARS (CARS-32) and Central Public-interest Scientific Institution Basal Research Fund (NO. 1630042022004).
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.