Next‐generation sequencing has greatly promoted the investigation of single nucleotide polymorphisms, while studies of simple sequence repeats are sharply decreasing. However, simple sequence repeats still present some advantages in conservation genetics. In this study, an end‐to‐end pipeline referred to as MultiplexSSR was established to develop multiplex PCR assays in batches with highly polymorphic simple sequence repeats for capillary platforms from resequencing data. The distribution of single sequence repeats in the genome, the error profiles of genotypes and allelotypes, and the increase in the allele length range depending on the number of individuals were investigated. A total of 98% of single sequence repeats presented lengths of less than 100 bp. The error rate of the genotyping and allelotyping of dimeric patterns was ten times higher than those for other patterns. The error rate of allelotyping was less than that of genotyping. The allele length range reached approximate saturation with 10 individuals. This pipeline uses allele numbers to select highly polymorphic loci, masks loci with variation, and applies in silico PCR to improve primer specificity. The application of the developed multiplex SSR‐PCR assays validated the pipeline's robustness, showing higher polymorphism and stability for the developed simple sequence repeats and a lower cost for genotyping and providing low‐depth resequencing data from less than a dozen individuals for the development of markers. This pipeline fills the gap between next‐generation sequencing and multiplex SSR‐PCR.

Grain weight is a key determinant of grain yield in rice. Three sets of rice populations with overlapping segregating regions in isogenic backgrounds were established in the generations of BC2F5, BC2F6 and BC2F7, derived from Zhenshan 97 and Milyang 46, and used for dissection of quantitative trait loci (QTL) for grain weight. Two QTL linked in repulsion phase on the long arm of chromosome 1 were separated. One was located between simple sequence repeat (SSR) markers RM11437 and RM11615, having a smaller additive effect with the enhancing allele from the maintainer line Zhenshan 97 and a partially dominant effect for increasing grain weight. The other was located between SSR markers RM11615 and RM11800, having a larger additive effect with the enhancing allele from the restorer line Milyang 46 and a partially dominant effect for increasing grain weight. When the two QTL segregated simultaneously, a residual additive effect with the enhancing allele from Milyang 46 and an over-dominance effect for increasing grain weight were detected. This suggests that dominant QTL linked in repulsion phase might play an important role in heterosis in rice. Our study also indicates that the use of populations with overlapping segregating regions in isogenic backgrounds is helpful for the dissection of minor linked QTL

The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.

Large-water fisheries are central to China’s freshwater aquaculture, but their sustainability is threatened by eutrophication from traditional high-density stocking. Polyculture of grass carp and crucian carp offers an ecologically sound alternative; nevertheless, its direct effects on plankton communities require further study. We conducted monthly sampling from July to December 2023 (over two seasons within a single aquaculture cycle) in polyculture ponds and used eDNA metabarcoding (18S V9) with high-throughput sequencing. We detected 288 planktonic taxa across 28 phyla and 290 genera based on eDNA sequence assignment. Alpha diversity (Chao1, Shannon, Simpson) peaked in autumn and was lowest in winter, with Chao1 showing greater seasonal variation. Beta diversity revealed season as the dominant factor (R² = 0.287, p = 0.012), with significant summer–winter divergence. Null-model analysis indicated stochastic processes (56.3%) slightly exceeded deterministic filtering (43.7%), and stochasticity was higher in summer (67.2%), suggesting fish bioturbation and grazing create heterogeneous microhabitats. Co-occurrence networks were dominated by positive links (87.3%), with Cryptomonas as a central hub, implying mutualism and niche complementarity. This study is the first to integrate eDNA metabarcoding with community assembly theory to elucidate seasonal succession and interactions in this polyculture. Our findings confirm that polyculture sustains diversity and stability via top-down (grazing) and bottom-up (nutrient release) effects, providing eDNA-based taxonomic evidence for management of large-water aquaculture.