Rootkin Joseph, Harrison-Tate Grace, Mayo-Riley Carol R, Matsumoto Tracie, Chapman Mark A
Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ UK.
Tropical Plant Genetic Resources & Disease Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, 64 Nowelo Street, 928 Stainback Highway, Hilo, HI 96720 USA.
Genet Resour Crop Evol. 2025;72(6):7373-7386. doi: 10.1007/s10722-025-02406-y. Epub 2025 Mar 18.
Lychee () 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.
The online version contains supplementary material available at 10.1007/s10722-025-02406-y.
荔枝果实具有很高的营养和药用价值，但由于其原生地区以外的种植问题以及对品种缺乏了解/误认，这种作物在全球市场上未得到充分利用。利用简化基因组测序技术，对美国农业部夏威夷荔枝种质库中代表57个品种的78棵树以及13棵无品种名称的树进行了分析。我们旨在：（1）了解遗传变异的分布；（2）确保同名品种的个体确实可能是同一 cultivar；（3）识别 cultivar 同义的情况。在去除具有大量缺失数据、稀有等位基因和低置信度单核苷酸多态性（SNP）后，对约10400个SNP进行了分析。遗传聚类和系统发育分析确定了两个主要组，根据现有数据，这两个组分别代表晚熟和极早熟品种，许多混合个体可能代表那些成熟期适中的品种。确定了用于品种鉴定的12个SNP核心集。来自同名品种的树并不总是密切相关，这代表存在误认。同样，一些具有不同品种名称的树似乎是相同的（即同义 cultivar）；在某些情况下，这证实了关于品种在不同国家之间运输和重新命名的现有知识。基于遗传相似性，我们发现了13组克隆，每组大小从2至9个个体不等。91棵树中有55棵（60%）属于这些组。总体而言，我们的数据有可能为荔枝种质资源的保护提供信息，并支持之前的研究结果，即主要有两个驯化基因库，第三组种质是混合的。展望未来，我们的结果可能会促进荔枝的改良，这是使其成为主粮作物的重要一步。
在线版本包含补充材料，可在10.1007/s10722-025-02406-y获取。
