Genetic diversity and population structure of the native grass carp ( Ctenopharyngodon idella ) from the Xiangjiang River revealed by microsatellite markers

Abstract

To investigate the genetic diversity and population structure of native grass carp ( Ctenopharyngodon idella ) in the Xiangjiang River, 16 highly polymorphic microsatellite markers were selected from the grass carp genome for a population genetic analysis of 300 individuals collected from a single section (Xiangluzhou) of the river, representing six different year‐classes (2016–2022). A total of 322 alleles were detected, with fragment sizes ranging from 126 to 314 bp. All 16 loci were highly polymorphic. The six year‐classes exhibited high levels of genetic diversity: the number of alleles ( N a ) ranged from 12.688 to 16.375 (mean = 14.927), the effective number of alleles ( N e ) from 7.160 to 9.115 (mean = 8.239), observed heterozygosity ( H o ) from 0.868 to 0.906 (mean = 0.889), expected heterozygosity ( H e ) from 0.853 to 0.881 (mean = 0.867), polymorphism information content (PIC) from 0.8367 to 0.8705 (mean = 0.8541) and allelic richness ( A r ) from 12.651 to 16.315 (mean = 14.867). Analysis of molecular variance (AMOVA) revealed that 98.19% of the total genetic variation resided within populations, whereas only 1.81% occurred among populations, indicating weak genetic differentiation. Both unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree and principal coordinate analysis (PCoA) consistently showed a closer genetic relationship between GC2021 and GC2016, and a relatively more distant relationship for GC2017 and GC2022. Structure analysis suggested an optimal clustering at K = 10, revealing an admixed genetic structure with subtle temporal differentiation among year‐classes, indicating diverse genetic compositions across cohorts. Bottleneck analysis provided suggestive evidence of historical population size reductions, but no strong signals of recent genetic bottlenecks were detected. Estimates of effective population size ( N E ) using the linkage disequilibrium method (the minor allele frequency threshold is 0.02) ranged from 16.9 to 111.3 across year‐classes, with a mean of 54.83. Although some year‐classes exhibited low N E values, the high gene flow among cohorts may mitigate associated inbreeding risk. These findings provide a scientific basis for the conservation and sustainable utilization of native Xiangjiang grass carp, with important implications for maintaining aquatic biodiversity in the Xiangjiang River and supporting the development of aquaculture industry.

Bibliographic Information