Genetic variation and synonymous cultivars in the USDA lychee (Litchi chinensis Sonn.) collection assessed using genome-wide SNPs.

Abstract

Lychee (Litchi chinensis) fruits have high nutritional and pharmacological value, yet the crop is underutilized on global markets partly due to cultivation problems outside the native area and lack of knowledge/misidentification of cultivars. Using reduced representation sequencing, 78 trees representing 57 cultivars plus 13 trees without varietal names from the USDA lychee collection on Hawai'i were analysed. We aimed to (1) understand the distribution of genetic variation, (2) ensure individuals of the same named variety were indeed likely the same cultivar, and (3) to identify cases of cultivar synonymy. After removing single nucleotide polymorphisms (SNPs) with substantial missing data, rare alleles and low confidence SNPs, analysis of ca. 10,400 SNPs was carried out. Genetic clustering and phylogenetic analysis identified two main groups which, based on existing data, represent the late and extremely early maturing cultivars, with many admixed individuals likely representing those with intermediate maturity times. A core set of 12 SNPs for cultivar identification were identified. Trees from the same named variety were not always closely related, representing misidentification. Similarly, some trees with different varietal names appear to be the same (i.e., synonymous cultivars); in some cases, this backed up existing knowledge about the transport and renaming of cultivars between countries. Based on genetic similarity, we found 13 groups of clones varying in size from 2-9 individuals. Fifty-five of the 91 trees (60%) were in these groups. Together, our data has the potential to inform the conservation of lychee accessions and backs up previous work that there are primarily two domesticated gene pools with a third group of accessions being admixed. Going forward, our results could lead to the improvement of lychee, a step in making it a staple crop.

Supplementary information: The online version contains supplementary material available at 10.1007/s10722-025-02406-y.