{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T13:10:50Z","timestamp":1788786650306,"version":"build-2803163510"},"reference-count":46,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Forestry and Grassland Administration of Xinjiang Forestry and Grassland Bureau","award":["XJLYKJ-2023-15"],"award-info":[{"award-number":["XJLYKJ-2023-15"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Caragana acanthophylla Kom. is an ecologically important drought-tolerant shrub in Xinjiang, China, but species-specific molecular markers for germplasm characterization remain limited. We sampled 93 individuals from 11 localities representing the currently known distribution of C. acanthophylla in Xinjiang. Three individuals per locality (33 in total) were whole-genome resequenced, yielding 2,873,410 high-quality SNPs and 5,679,915 InDels. Genome-wide SNP-based PCA and genetic relationship analysis provided an independent high-resolution assessment of the 33 resequenced individuals. From 34 candidate primer pairs, eight polymorphic InDel markers with stable amplification and clear genotyping profiles were retained and applied to all 93 individuals. The SNP dataset revealed clear regional differentiation and finer locality-associated relationships. Analysis of the same 33 individuals with the eight InDel loci recovered part of this broad pattern, particularly the differentiation of the western YL materials, but showed lower fine-scale resolution. Across all 93 individuals, the InDel panel revealed moderate to low marker-level genetic diversity and detectable regional differentiation. AMOVA attributed 67.00% of the variation to differences among the 11 original sampling localities, while the five exploratory analytical groups showed a similar among-group component (68.37%). The Mantel correlation detected across all 93 individuals (r = 0.801, p &lt; 0.001) disappeared after YL was excluded (r = \u22120.032, p = 0.724), indicating that the overall spatial signal was largely driven by the geographic separation of YL. These results support the eight-marker panel as a practical, low-cost tool for preliminary germplasm characterization and broader sample screening, while genome-wide SNP data provide substantially greater resolution for population-level inference.<\/jats:p>","DOI":"10.3390\/plants15172733","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T12:12:25Z","timestamp":1788783145000},"page":"2733","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development of Genome-Derived InDel Markers and Genetic Diversity Analysis of Caragana acanthophylla in Xinjiang, China"],"prefix":"10.3390","volume":"15","author":[{"given":"Yinjuan","family":"Yao","sequence":"first","affiliation":[{"name":"College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Zhenfan","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Haojie","family":"Bi","sequence":"additional","affiliation":[{"name":"College of Landscape Architecture and Tourism Management, Xinjiang Applied Vocational Technical College, Kuitun 833200, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Mingzhi","family":"Du","sequence":"additional","affiliation":[{"name":"College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Abasi","family":"Abudouwaili","sequence":"additional","affiliation":[{"name":"College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Shiji","family":"Gong","sequence":"additional","affiliation":[{"name":"College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Junhua","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"ref_1","first-page":"600","article-title":"Molecular phylogeny of Caragana (Fabaceae) in China","volume":"46","author":"Hou","year":"2008","journal-title":"J. Syst. Evol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.ympev.2008.12.001","article-title":"Phylogeny of Caragana (Fabaceae) based on DNA sequence data from rbcL, trnS-trnG, and ITS","volume":"50","author":"Zhang","year":"2009","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"111","DOI":"10.3897\/phytokeys.70.9641","article-title":"A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations","volume":"70","author":"Duan","year":"2016","journal-title":"PhytoKeys"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Cui, X., Liu, K., Li, E., Zhang, Z., and Dong, W. (2024). Chloroplast genomes evolution and phylogenetic relationships of Caragana species. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25126786"},{"key":"ref_5","first-page":"47","article-title":"Effects of different substrates and transplanting periods on the growth of Caragana acanthophylla","volume":"1","author":"Aierken","year":"2023","journal-title":"Heilongjiang Agric. Sci."},{"key":"ref_6","first-page":"2307","article-title":"Effects of different fertilization ratios on seedling quality of Caragana acanthophylla","volume":"53","author":"Liu","year":"2016","journal-title":"Xinjiang Agric. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1093\/jpe\/rtx062","article-title":"Species richness and composition of shrub-encroached grasslands in relation to environmental factors in northern China","volume":"12","author":"Zhou","year":"2019","journal-title":"J. Plant Ecol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e6870","DOI":"10.7717\/peerj.6870","article-title":"Water permeability\/impermeability in seeds of 15 species of Caragana (Fabaceae)","volume":"7","author":"Chen","year":"2019","journal-title":"PeerJ"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.3724\/SP.J.1145.2015.05001","article-title":"Effects of dry storage duration on seed germination of Caragana acanthophylla and C. roborovskyi","volume":"21","author":"Wang","year":"2015","journal-title":"Chin. J. Appl. Environ. Biol."},{"key":"ref_10","first-page":"513","article-title":"Responses of seed viability and germination of four Caragana species in Xinjiang to burial under snow","volume":"41","author":"Halimulati","year":"2023","journal-title":"Plant Sci. J."},{"key":"ref_11","first-page":"528","article-title":"Caragana","volume":"Volume 10","author":"Wu","year":"2010","journal-title":"Flora of China"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1007\/BF00120641","article-title":"Factors influencing levels of genetic diversity in woody plant species","volume":"6","author":"Hamrick","year":"1992","journal-title":"New For."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1098\/rstb.1996.0112","article-title":"Effects of life history traits on genetic diversity in plant species","volume":"351","author":"Hamrick","year":"1996","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_14","first-page":"4872","article-title":"Seed selective abortion pattern under the influence of two reciprocal resource gradients in Caragana acanthophylla","volume":"42","author":"Wang","year":"2022","journal-title":"Acta Ecol. Sin."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1111\/j.1558-5646.1965.tb01731.x","article-title":"The interpretation of population structure by F-statistics with special regard to systems of mating","volume":"19","author":"Wright","year":"1965","journal-title":"Evolution"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1073\/pnas.70.12.3321","article-title":"Analysis of gene diversity in subdivided populations","volume":"70","author":"Nei","year":"1973","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"8256","DOI":"10.1002\/ece3.2549","article-title":"Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin Sandy Land, northeast China","volume":"6","author":"Huang","year":"2016","journal-title":"Ecol. Evol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Xu, B., Sun, G., Wang, X., Lu, J., Wang, I.J., and Wang, Z. (2017). Population genetic structure is shaped by historical, geographic, and environmental factors in the leguminous shrub Caragana microphylla on the Inner Mongolia Plateau of China. BMC Plant Biol., 17.","DOI":"10.1186\/s12870-017-1147-7"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.2135\/cropsci2006.09.0562","article-title":"Genetic diversity and population structure of Caragana korshinskii revealed by AFLP","volume":"47","author":"Wang","year":"2007","journal-title":"Crop Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1134\/S1022795411090043","article-title":"Genetic variability and differentiation of Caragana microphylla populations as revealed by RAPD markers","volume":"47","author":"Chen","year":"2011","journal-title":"Russ. J. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"V\u00e4li, \u00dc., Brandstr\u00f6m, M., Johansson, M., and Ellegren, H. (2008). Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genet., 9.","DOI":"10.1186\/1471-2156-9-8"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Sahu, P.K., Mondal, S., Sharma, D., Vishwakarma, G., Kumar, V., and Das, B.K. (2017). InDel marker based genetic differentiation and genetic diversity in traditional rice (Oryza sativa L.) landraces of Chhattisgarh, India. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0188864"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1093\/dnares\/dsv020","article-title":"Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea","volume":"22","author":"Das","year":"2015","journal-title":"DNA Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2454","DOI":"10.1111\/nph.70360","article-title":"Ancient hybridization drives arid adaptation and species diversification in Caragana (Fabaceae)","volume":"247","author":"Cui","year":"2025","journal-title":"New Phytol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Song, J., An, J., Xia, H., Li, W., Hu, J., Li, Q., Li, C., Shen, X., Cheng, H., and Zhou, Y. (2026). Pan-genome analysis of Caragana reveals genomic mechanisms of drought adaptation of leguminous shrubs to arid environments. Genome Biol., early access.","DOI":"10.1186\/s13059-026-04230-8"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1126\/science.3576198","article-title":"Gene flow and the geographic structure of natural populations","volume":"236","author":"Slatkin","year":"1987","journal-title":"Science"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1146\/annurev.es.24.110193.001245","article-title":"Population genetic consequences of small population size: Implications for plant conservation","volume":"24","author":"Ellstrand","year":"1993","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1111\/jse.12088","article-title":"Plant phylogeography in arid Northwest China: Retrospectives and perspectives","volume":"53","author":"Meng","year":"2015","journal-title":"J. Syst. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/evo.12258","article-title":"Genetic isolation by environment or distance: Which pattern of gene flow is most common?","volume":"68","author":"Sexton","year":"2014","journal-title":"Evolution"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1111\/mec.12938","article-title":"Isolation by environment","volume":"23","author":"Wang","year":"2014","journal-title":"Mol. Ecol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"103957","DOI":"10.1016\/j.earscirev.2022.103957","article-title":"Recent climate and hydrological changes in a mountain-basin system in Xinjiang, China","volume":"226","author":"Yao","year":"2022","journal-title":"Earth-Sci. Rev."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1080\/14772000.2019.1612966","article-title":"Phylogeography suggest the Yili Valley being the glacial refuge of the genus Ixiolirion (Amaryllidaceae) in China","volume":"17","author":"Li","year":"2019","journal-title":"Syst. Biodivers."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1111\/jbi.13999","article-title":"Insights into the aridification history of central Asian mountains and international conservation strategy from the endangered wild apple tree","volume":"48","author":"Zhang","year":"2021","journal-title":"J. Biogeogr."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3258","DOI":"10.1111\/evo.12193","article-title":"Disentangling the effects of geographic and ecological isolation on genetic differentiation","volume":"67","author":"Bradburd","year":"2013","journal-title":"Evolution"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.biocon.2005.05.002","article-title":"Genetics and extinction","volume":"126","author":"Frankham","year":"2005","journal-title":"Biol. Conserv."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.biocon.2014.06.014","article-title":"Optimal sampling of seeds from plant populations for ex-situ conservation of genetic biodiversity, considering realistic population structure","volume":"177","author":"Hoban","year":"2014","journal-title":"Biol. Conserv."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"108654","DOI":"10.1016\/j.biocon.2020.108654","article-title":"Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved","volume":"248","author":"Hoban","year":"2020","journal-title":"Biol. Conserv."},{"key":"ref_38","unstructured":"Editorial Committee of Flora Xinjiangensis (2019). Flora Xinjiangensis, Xinjiang People\u2019s Publishing House. (In Chinese)."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1093\/bioinformatics\/bts460","article-title":"GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update","volume":"28","author":"Peakall","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_41","unstructured":"Sneath, P.H.A., and Sokal, R.R. (1973). Numerical Taxonomy: The Principles and Practice of Numerical Classification, W. H. Freeman."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study","volume":"14","author":"Evanno","year":"2005","journal-title":"Mol. Ecol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method","volume":"4","author":"Earl","year":"2012","journal-title":"Conserv. Genet. Resour."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","article-title":"GCTA: A Tool for Genome-wide Complex Trait Analysis","volume":"88","author":"Yang","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_46","unstructured":"(2026, August 31). TreeBeST: Tree Building Guided by Species Tree, Version 1.9.2. Available online: http:\/\/treesoft.sourceforge.net\/treebest.shtml."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/17\/2733\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T12:46:27Z","timestamp":1788785187000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/17\/2733"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,7]]},"references-count":46,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["plants15172733"],"URL":"https:\/\/doi.org\/10.3390\/plants15172733","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,7]]}}}