Characterization of Chromosomal Structural Polymorphism in Roegneria nutans from the Western Sichuan Plateau, China Based on Tandem Repeat Sequences

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’ 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.