ArticleBMC plant biology2025
Low-density SNP marker sets for genetic variation analysis and variety identification in cultivated citrus.
Article in BMC plant biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Chromosome-scale assembly of the eliteHorticulture research · 2026Article
- SSR marker development for analysis of the genetic diversity and identification of species and infraspecific ranks in the genus Phyllostachys.BMC plant biology · 2026Article
- Integrated morphological, pomological, biochemical, and ISSR-based assessment of genetic diversity in wild sour orange (Citrus aurantium L.) genotypes from the Hassa district of Hatay, Türkiye.Biological research · 2026Article
- Dissecting genetic diversity and population structure in intergeneric citrus population using morphological and SSR markers.Scientific reports · 2026Article
- Comprehensive transposon-insertion profiling unravels the asexual breeding history of sweet orange cultivars.Plant communications · 2025Article
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4 authors.
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Abstract
backgroundThe Citrus species are major fruit crops cultivated in the world and have complex genetic relationships due to sexual comparability between Citrus and related genera. Of these, satsuma mandarin (C. unshiu (Mak.) Marc.) and sweet orange (C. sinensis (L.) Osb.) are widely grown diploid species. In this study, genotyping by sequencing (GBS) was conducted to identify single nucleotide polymorphisms (SNPs) for investigating genetic variation in a citrus collection.
resultsA total of 26,903 high-quality SNPs were detected across nine chromosomes in the 144 citrus varieties, consisting of 70 C. unshiu, 40 C. sinensis, 22 interspecific hybrids, and 12 others. Of these, a core set of 481 SNPs was filtered based on polymorphism information content and genome distribution. Both principal component analysis (PCA) and model-based clustering showed genetic differentiation between C. unshiu and C. sinensis. For interspecific hybrids, these were separated from two species in PCA, but were mixed with each species in model-based clustering. Significant genetic differentiations between three populations were also found using the pairwise F
conclusionsThe GBS-based SNP discovery led to robust and cost-effective molecular marker sets to assess genetic variation in the cultivated citrus species with narrow genetic bases. The resulting SNP sets are a resource to enhance the phenotype-based DUS testing by developing a DNA barcode system and thus facilitate new variety breeding and protection in citrus.
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