{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T19:41:03Z","timestamp":1783453263151,"version":"3.55.0"},"reference-count":60,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Open Research Project from Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources","award":["2023TSYY-09"],"award-info":[{"award-number":["2023TSYY-09"]}]},{"name":"Chengdu Science and Technology Bureau Technological Innovation and R&D Project","award":["2025-YF05-00613-SN"],"award-info":[{"award-number":["2025-YF05-00613-SN"]}]},{"name":"High-Level Talent Introduction Program of Chengdu Normal University","award":["YJRC2020-23"],"award-info":[{"award-number":["YJRC2020-23"]}]},{"name":"Chengdu Normal University Key Program Project","award":["TSYY202402"],"award-info":[{"award-number":["TSYY202402"]}]},{"name":"College Students\u2019 Innovation and Entrepreneurship Training Programs","award":["202414389020"],"award-info":[{"award-number":["202414389020"]}]},{"name":"College Students\u2019 Innovation and Entrepreneurship Training Programs","award":["202414389030"],"award-info":[{"award-number":["202414389030"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Dendrobium officinale, a perennial epiphytic herb of the orchid family renowned for its ornamental value and diverse medicinal properties, has attracted considerable global attention due to its rarity and increasing market demand. However, large-scale cultivation has led to confusion regarding its germplasm resources and genetic backgrounds, posing significant challenges for the effective conservation, management, and utilization of D. officinale germplasm. In this study, we systematically analyzed the abundance and characteristics of simple sequence repeats (SSRs) and developed highly polymorphic genomic SSR markers using whole-genome resequencing (WGRS) data from 15 D. officinale genotypes. A total of 494,783 SSRs were identified in the \u201cNiu2020\u201d reference genome. Mononucleotide repeats were the most abundant motifs, followed by dinucleotide repeats, with A\/T and AT\/TA being the predominant types, respectively. Of the SSRs with unique flanking sequences (unique SSRs), 121,544 out of 388,553 (31.28%) were polymorphic across the 15 genotypes. The polymorphism information content (PIC) values of these SSRs ranged from 0.13 to 0.92, with an average of 0.59. Subsequently, 10,364 pairs of SSR primers were successfully designed from polymorphic SSR loci with PIC values \u2265 0.5 and major allele size differences \u2265 3 bp. Ultimately, 20 primer pairs were randomly selected for experimental validation. Of these, 18 successfully amplified the target fragments and exhibited high levels of polymorphism (PIC values ranged from 0.31 to 0.74), confirming the effectiveness and practical utility of the newly developed markers. The SSR fingerprints and polymorphic markers developed in this study provide a valuable resource and establish a robust technical foundation for enhancing the efficiency of cultivar identification, genetic research, and molecular breeding in D. officinale.<\/jats:p>","DOI":"10.3390\/plants14233589","type":"journal-article","created":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T10:46:18Z","timestamp":1764067578000},"page":"3589","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genome-Wide Discovery of SSR Markers Based on Whole-Genome Resequencing Data of Dendrobium officinale"],"prefix":"10.3390","volume":"14","author":[{"given":"Mingmin","family":"Zheng","sequence":"first","affiliation":[{"name":"Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu 611130, China"},{"name":"College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Mi","sequence":"additional","affiliation":[{"name":"Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pingrong","family":"Zhou","sequence":"additional","affiliation":[{"name":"Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Li","sequence":"additional","affiliation":[{"name":"Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yelin","family":"Wang","sequence":"additional","affiliation":[{"name":"Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Liu","sequence":"additional","affiliation":[{"name":"Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Jiang","sequence":"additional","affiliation":[{"name":"Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu 611130, China"},{"name":"College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"He, Y., Li, L., Chang, H., Cai, B., Gao, H., Chen, G., Hou, W., Jappar, Z., and Yan, Y. 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