{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T15:30:45Z","timestamp":1789659045434,"version":"4.0.1"},"reference-count":51,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200196"],"award-info":[{"award-number":["32200196"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32200196"],"award-info":[{"award-number":["32200196"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Technological Innovation and R&D Project of the Science and Technology Bureau of Chengdu","award":["2026-YF05-00439-SN"],"award-info":[{"award-number":["2026-YF05-00439-SN"]}]},{"name":"Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources","award":["2024TSYY202402Z"],"award-info":[{"award-number":["2024TSYY202402Z"]}]},{"name":"High-Level Scientific Research Project Cultivation Special Fund of Chengdu Normal University","award":["CS22XMPY0106"],"award-info":[{"award-number":["CS22XMPY0106"]}],"id":[{"id":"https:\/\/ror.org\/04enz2k98","id-type":"ROR","asserted-by":"crossref"}]},{"award":["CS22XMPY0106"],"award-info":[{"award-number":["CS22XMPY0106"]}],"id":[{"id":"https:\/\/ror.org\/04enz2k98","id-type":"ROR","asserted-by":"publisher"}]},{"name":"College Students\u2019 Innovation and Entrepreneurship Training Program","award":["S202614389077"],"award-info":[{"award-number":["S202614389077"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Roegneria nutans, a premium grass on Western Sichuan Plateau, China, is vital for ecological stability and pastoral security. Studying its chromosomal architecture and environmental correlations lays a foundation for Roegneria genetic evolution research. This study used genomic in situ hybridization (GISH) and non-denaturing fluorescence in situ hybridization (ND-FISH) with two tandem repetitive sequence probes pAs1 and (AAG)10) to analyze the species\u2019 St and Y genomes of R. nutans from different altitudes. Our findings demonstrated that for both the number of probe signals and variant types, inter-population variation was higher than intra-population variation. Distinct altitudinal response patterns of (AAG)10 and pAs1 FISH signals were detected between the St and Y genomes. Within the St genome, the abundance of (AAG)10 loci exhibited a trend of initial decline followed by a marked rise with increasing altitude. The pAs1 probe displayed higher signal density than (AAG)10, with its signal abundance peaking in medium-altitude populations, and polymorphic loci were most abundant in high-altitude populations. In contrast, medium-altitude samples harboured relatively fewer (AAG)10 signals within the Y genome. Although pAs1 exhibited lower signal density than (AAG)10 in the Y genome, its maximum signal number was observed in medium-altitude populations, where polymorphic loci predominated. Low-altitude populations maintained relatively conserved hybridization patterns, and chromosomal variation was mainly detected in the Y genome at medium altitudes and in the St genome at high altitudes. This study provides a valuable basis for exploring the genetic diversity of R. nutans across the Western Sichuan Plateau.<\/jats:p>","DOI":"10.3390\/plants15182832","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T07:58:59Z","timestamp":1789545539000},"page":"2832","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Characterization of Chromosomal Structural Polymorphism in Roegneria nutans from the Western Sichuan Plateau, China Based on Tandem Repeat Sequences"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7553-0039","authenticated-orcid":false,"given":"Cairong","family":"Yang","sequence":"first","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"},{"name":"Sichuan Provincial Forestry and Grassland Key Laboratory of Biodiversity Conservation and Sustainable Community Development in Giant Panda National Park, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]},{"given":"Yueju","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Yi","family":"Ou","sequence":"additional","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Zhimeng","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Yutong","family":"Qiao","sequence":"additional","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Dingfang","family":"Luo","sequence":"additional","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Jiaping","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Xin","family":"Lin","sequence":"additional","affiliation":[{"name":"College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Jiezhi","family":"Yang","sequence":"additional","affiliation":[{"name":"Neijiang Academy of Agricultural Sciences, Neijiang 641000, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1360\/N972017-00125","article-title":"What determines species diversity?","volume":"62","author":"Ge","year":"2017","journal-title":"Chin. Sci. Bull."},{"key":"ref_2","first-page":"297","article-title":"Biodiversity hotspots: A shortcut for a more complicated concept","volume":"3","author":"Marchese","year":"2015","journal-title":"Glob. Ecol. Conserv."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1126\/science.abb4484","article-title":"Ancient orogenic and monsoon-driven assembly of the world\u2019s richest temperate alpine flora","volume":"369","author":"Ding","year":"2020","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"8114","DOI":"10.1038\/s41598-022-12175-8","article-title":"Spatio-temporal evolution and driving factors of carbon storage in the Western Sichuan Plateau","volume":"12","author":"Xiang","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_5","first-page":"289","article-title":"Beitr\u00e4ge zu einer Flora des Orients","volume":"21","author":"Koch","year":"1848","journal-title":"Linnaea"},{"key":"ref_6","unstructured":"Yen, C., and Yang, J.L. (2011). Biosystematics of Triticeae, China Agricultural Press. (In Chinese)."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1111\/j.1601-5223.1990.tb00074.x","article-title":"Genomic constitution of Elymus parviglumis and E. pseudonutans: Triticeae (Poaceae)","volume":"113","author":"Lu","year":"1990","journal-title":"Hereditas"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1139\/g90-099","article-title":"Cytology and taxonomy of Elymus kengii, E. grandiglumis, E. alatavicus, and E. batalinii (Poaceae: Triticeae)","volume":"33","author":"Jensen","year":"1990","journal-title":"Genome"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1111\/jse.12084","article-title":"Biosystematics and evolutionary relationships of perennial Triticeae species revealed by genomic analyses","volume":"52","author":"Wang","year":"2014","journal-title":"J. Syst. Evol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Dewey, D.R. (1984). The genomic system of classification as a guide to intergeneric hybridization with the perennial Triticeae. Gene Manipulation in Plant Improvement, Springer New York, NY, USA.","DOI":"10.1007\/978-1-4613-2429-4_9"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.ympev.2010.03.037","article-title":"Origin of the Y genome in Elymus and its relationship to other genomes in Triticeae based on evidence from elongation factor G (EF-G) gene sequences","volume":"56","author":"Sun","year":"2010","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.ympev.2015.02.012","article-title":"Molecular phylogeny revealed distinct origin of the Y and St genome in Elymus longearistatus (Triticeae: Poaceae)","volume":"85","author":"Hu","year":"2015","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1111\/j.1469-8137.2006.01665.x","article-title":"Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences","volume":"170","author":"Liu","year":"2006","journal-title":"New Phytol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1093\/plphys\/kiae433","article-title":"Chromosome-specific painting reveals the Y genome origin and chromosome rearrangements of the St genome in Triticeae","volume":"196","author":"Chen","year":"2024","journal-title":"Plant Physiol."},{"key":"ref_15","unstructured":"Stebbins, G.L. (1971). Chromosomal Evolution in Higher Plants, Edward Arnold LTD."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1080\/07352689309701903","article-title":"Molecular data and the dynamic nature of polyploidy","volume":"12","author":"Soltis","year":"1993","journal-title":"Crit. Rev. Plant Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1111\/nph.15357","article-title":"Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval","volume":"221","author":"Cai","year":"2019","journal-title":"New Phytol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1093\/aob\/mcz070","article-title":"Role of ploidy in colonization of alpine habitats in natural populations of Arabidopsis arenosa","volume":"124","author":"Wos","year":"2019","journal-title":"Ann. Bot."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.17520\/biods.2021146","article-title":"A comparison of seed plants\u2019 polyploids between the Qinghai-Tibet Plateau alpine and the Pan-Arctic regions","volume":"29","author":"Zhang","year":"2021","journal-title":"Biodivers. Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41559-018-0787-9","article-title":"The global biogeography of polyploid plants","volume":"3","author":"Rice","year":"2019","journal-title":"Nat. Ecol. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/aob\/mcac021","article-title":"Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids","volume":"130","author":"Moraes","year":"2022","journal-title":"Ann. Bot."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Wang, Q.X., Liu, H.T., Gao, A.N., Yang, X.M., Liu, W.H., Li, X.Q., and Li, L.H. (2012). Intergenomic rearrangements after polyploidization of Kengyilia thoroldiana (Poaceae: Triticeae) affected by environmental factors. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0031033"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1139\/gen-2016-0199","article-title":"Genomic constitution and intergenomic translocations in the Elymus dahuricus complex revealed by multicolor GISH","volume":"60","author":"Yang","year":"2017","journal-title":"Genome"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Chen, Z., Guan, Y., Han, M., Guo, Y., Zhang, J., Guo, Z., Sun, G., and Yan, X. (2022). Altitudinal patterns in adaptive evolution of genome size and inter-genome hybridization between three Elymus species from the Qinghai-Tibet Plateau. Front. Ecol. Evol., 10.","DOI":"10.3389\/fevo.2022.923967"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2453","DOI":"10.1046\/j.1365-294X.2002.01643.x","article-title":"Microsatellites: Genomic distribution, putative functions and mutational mechanisms: A review","volume":"11","author":"Li","year":"2002","journal-title":"Mol. Ecol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1146\/annurev-genet-072610-155046","article-title":"Variable tandem repeats accelerate evolution of coding and regulatory sequences","volume":"44","author":"Gemayel","year":"2010","journal-title":"Annu. Rev. Genet."},{"key":"ref_27","first-page":"203","article-title":"Slipped-strand mispairing: A major mechanism for DNA sequence evolution","volume":"4","author":"Levinson","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"10552","DOI":"10.1038\/srep10552","article-title":"Oligonucleotide probes for ND-FISH analysis to identify rye and wheat chromosomes","volume":"5","author":"Fu","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_29","first-page":"859","article-title":"Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution?","volume":"100","author":"Grover","year":"2011","journal-title":"Curr. Sci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1111\/nph.70173","article-title":"Simple sequence repeats and their expansions: Role in plant development, environmental response and adaptation","volume":"247","author":"Sureshkumar","year":"2025","journal-title":"New Phytol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e70370","DOI":"10.1111\/tpj.70370","article-title":"Comprehensive identification and analysis of clusters of tandemly duplicated genes reveal their contributions to adaptive evolution of green plants","volume":"123","author":"Yang","year":"2025","journal-title":"Plant J."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Jiang, C., Liu, X., Yang, Z., and Li, G. (2023). Chromosome rearrangement in Elymus dahuricus Revealed by ND-FISH and Oligo-FISH Painting. Plants, 12.","DOI":"10.3390\/plants12183268"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"375","DOI":"10.3897\/compcytogen.v15.i4.71525","article-title":"The Kengyilia hirsuta karyotype polymorphisms as revealed by FISH with tandem repeats and single-gene probes","volume":"15","author":"Tao","year":"2021","journal-title":"Comp. Cytogenet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1139\/gen-2017-0046","article-title":"Characterization of genome in tetraploid StY species of Elymus (Triticeae: Poaceae) using sequential FISH and GISH","volume":"60","author":"Liu","year":"2017","journal-title":"Genome"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.pld.2017.05.003","article-title":"High molecular karyotype variation revealed in indigenous Elymus nutans in the Qinghai Plateau","volume":"39","author":"Dou","year":"2017","journal-title":"Plant Divers."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/j.pld.2021.12.003","article-title":"Molecular cytogenetic study on the plants of Elymus nutans with varying fertility on the Qinghai-Tibet Plateau","volume":"44","author":"Liu","year":"2022","journal-title":"Plant Divers."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1111\/gfs.12646","article-title":"Evaluation of chromosome diversity of Elymus nutans on the Qinghai-Tibet plateau by FISH","volume":"79","author":"Liu","year":"2024","journal-title":"Grass Forage Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1139\/G09-098","article-title":"Analysis of chromosomal structural polymorphisms in the St, P, and Y genomes of Triticeae (Poaceae)","volume":"53","author":"Wang","year":"2010","journal-title":"Genome"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e71332","DOI":"10.1002\/ece3.71332","article-title":"Environmental data do not correlate with plant genetic diversity in alpine ecosystems","volume":"15","author":"Fajardo","year":"2025","journal-title":"Ecol. Evol."},{"key":"ref_40","first-page":"647","article-title":"Gradual evolution of a specific satellite DNA family in Drosophila ambigua, D. tristis, and D. obscura","volume":"10","author":"Bachmann","year":"1993","journal-title":"Mol. Biol. Evol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Tang, J.F., Baldwin, S.J., Jacobs, J.M., van der Linden, C.G., Voorrips, R.E., Jack, A.M., Leunissen, J.A., van Eck, H., and Vosman, B. (2008). Large-scale identification of polymorphic microsatellites using an in silico approach. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-374"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1139\/G10-091","article-title":"Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid","volume":"54","author":"Yaakov","year":"2011","journal-title":"Genome"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1534\/genetics.104.039263","article-title":"Rapid and repeatable elimination of a parental genome-specific DNA repeat (pGc1R-1a) in newly synthesized wheat allopolyploids","volume":"170","author":"Han","year":"2005","journal-title":"Genetics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1007\/s00606-005-0384-7","article-title":"Genome size in Bulgarian Centaurea s.l. (Asteraceae)","volume":"257","author":"Bancheva","year":"2006","journal-title":"Plant Syst. Evol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s10592-008-9596-z","article-title":"Intra-population genetic diversity of two wheatgrass species along altitude gradients on the Qinghai-Tibetan Plateau: Its implication for conservation and utilization","volume":"10","author":"Yan","year":"2009","journal-title":"Conserv. Genet."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1515\/sg-2014-0025","article-title":"Genetic diversity of Picea likiangensis natural population at different altitudes revealed by EST-SSR markers","volume":"63","author":"Cheng","year":"2014","journal-title":"Silvae Genet."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1111\/nph.18744","article-title":"Hidden genetic variation in plasticity provides the potential for rapid adaptation to novel environments","volume":"239","author":"Walter","year":"2023","journal-title":"New Phytol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1007\/s11103-022-01326-0","article-title":"Genetic diversity and gene expression diversity shape the adaptive pattern of the aquatic plant Batrachium bungei along an altitudinal gradient on the Qinghai-Tibet plateau","volume":"111","author":"Yu","year":"2023","journal-title":"Plant Mol. Biol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"msae155","DOI":"10.1093\/molbev\/msae155","article-title":"Biased retention of environment-responsive genes following genome fractionation","volume":"41","author":"Beringer","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"e9677","DOI":"10.1002\/ece3.9677","article-title":"Biased gene expression reveals the contribution of subgenome to altitude adaptation in allopolyploid Isoetes sinensis","volume":"12","author":"Wei","year":"2022","journal-title":"Ecol. Evol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/plcell\/koaa015","article-title":"Polyploidy: An evolutionary and ecological force in stressful times","volume":"33","author":"Ashman","year":"2021","journal-title":"Plant Cell"}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2832\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T08:49:15Z","timestamp":1789548555000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2832"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":51,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["plants15182832"],"URL":"https:\/\/doi.org\/10.3390\/plants15182832","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]}}}