ArticleBMC plant biology2025
RAD-Seq-derived SSR markers: a new paradigm for genetic analysis and construction of genetically improved production populations in Pinus koraiensis.
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 1 paper.
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Abstract
backgroundThe principal objective of this research is to develop highly specific polymorphic molecular markers, with the aim of addressing the paucity of simple sequence repeat (SSR) markers in Pinus koraiensis. The objective of this initiative is to facilitate the efficient management of genetic resources within Pinus koraiensis, enable precise pedigree identification and establish a foundational framework for subsequent whole-genome sequencing and assembly strategies. To achieve this objective, a simplified genome sequencing approach was employed, utiliZing RAD-Seq technology on a sample of 100 clones of Pinus koraiensis sourced from 6 seed orchards. The SSR sequences present within the contig were identified via TBtools-II software, which was also employed to generate a comprehensive summary and analysis of the sequence characteristics. On the Basis of these insights, primers were designed and subjected to meticulous screening using bioinformatics methodologies, and their efficacy was subsequently verified. The SSR markers were subsequently employed to examine the genetic diversity and structure of the plus tree population. The genetic data were then integrated with multiyear cone production records from the population of plus trees, thus facilitating the construction of a production population.
resultsA total of 80,539 SSR sites were identified among the 5,840,917 reads that were subjected to analysis. Notably, that the majority of these SSRs were dinucleotide to trinucleotide repeats, constituting 93.838% of the total. As the number of repeats increased, a gradual decline in the number of SSRs was observed. The most prevalent repetitive motif within the SSR loci was (AT/TA)
conclusionsThe utilization of RAD-seq technology enables the development of SSR markers and the screening of polymorphic primers, thereby providing a robust tool for research pertaining to genetic diversity analysis and the identification of germplasm in Pinus koraiensis. The plus tree population in Xiaobeihu exhibits a considerable degree of genetic diversity, with no notable genetic differentiation. The construction of production populations via the developed SSR markers in combination with cone production from plus trees results in a reasonable population size and a mating system, thereby providing a scientific basis and technical support for the evaluation of Pinus koraiensis germplasm resources and advanced-generation improvement efforts. Furthermore, this study provides a reference and guidance for the development and application of SSR markers in other tree species.
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