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Analysis of SSR Loci and Development of Molecular Markers in Isatis indigotica Genome
SUNTianqi, ZHOULei, XULingui, SUNXiaobo, CHENYong, SUIChun
Chin Agric Sci Bull ›› 2026, Vol. 42 ›› Issue (2) : 50-56.
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Abbreviation (ISO4): Chin Agric Sci Bull
Editor in chief: Yulong YIN
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Analysis of SSR Loci and Development of Molecular Markers in Isatis indigotica Genome
In response to the lack of effective molecular markers for the identification of Isatis indigotica germplasm and the difficulty of distinguishing cultivated types within the species using existing methods, this study aimed to develop simple sequence repeat (SSR) molecular markers suitable for germplasm identification and genetic diversity analysis in I. indigotica. Based on whole-genome data of I. indigotica, SSR loci were screened using MISA software, and primers were designed with Primer3.0. Using three cultivated types of I. indigotica (comprising 18 individual plants) as experimental materials, the amplification stability, polymorphism, effectiveness, and variety identification ability of the primers were validated. Genetic diversity parameters were also calculated. The results showed that: (1) a total of 139,852 SSR loci were detected in the I. indigotica genome. The most abundant were mononucleotide SSR loci, accounting for approximately 72.51% of the total. The most frequent SSR motif, A/T, also exhibited the highest total number of repeats among all nucleotide SSR motifs, with a count of 100,205, accounting for 71.65% of all repeated motifs. (2) Eight pairs of primers that can stably amplify genes and have rich polymorphisms were screened out. Among them, primer SSRSL02 could be used to distinguish the I. indigotica germplasms tested in this study. (3) The eight primer pairs exhibited the average expected heterozygosity (He) of 0.65, the average Shannon's information index (I) of 1.34, and the average polymorphic information content (PIC) of 0.614, indicating a relatively high level of genetic diversity within the tested I. indigotica samples. In summary, the eight SSR molecular markers developed in this study can be used for the identification of I. indigotica germplasm resources, genetic diversity analysis, and variety breeding. In the future, the sample size of I. indigotica germplasm could be expanded, and DNA fingerprinting could be constructed by integrating phenotypic data and active ingredient content, thereby providing more comprehensive technical support for the precise evaluation of I. indigotica germplasm resources.
Isatis indigotica / SSR / molecular markers / polymorphism / genetic diversity / germplasm identification
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