Genomic selection, which uses genome-wide molecular markers to estimate breeding values, has become an essential tool in aquaculture breeding due to its high predictive accuracy. However, high genotyping cost and reduced model performance across populations and generations due to allele frequency change limit its practical application. Screening molecular markers with higher predictive accuracy and greater genetic stability is critical to reducing costs and improving performance. Histone modifications, as key epigenetic regulators, provide comprehensive information on cis-regulatory elements and chromatin states. This study presents an innovative histone modification-based SNP screening method for genomic selection of growth traits (body length) in Litopenaeus vannamei. Using resequencing and phenotypic data from 973 shrimp, genomic selection models (GBLUP, BayesA, BayesB, BayesC) were constructed. Prediction accuracy improved with increasing marker density, stabilizing after 20k SNPs, with BayesA achieving the highest accuracy (0.36 ± 0.01 at 30k SNPs). CUT&Tag technology was used to generate high-resolution profiles of H3K4me1, H3K4me3, H3K27me3, and H3K27ac from L. vannamei embryos at multiple developmental stages and adult muscle tissues. These profiles were used to annotate cis-regulatory elements across the genome, and SNPs in these regions were screened for predictions. In low-density intervals (0.5k-5k), SNPs in H3K4me1 and H3K4me3-enriched regions outperformed randomly selected SNPs, showing 5.56%-6.90% higher predictive accuracy and greater stability. Moreover, integrating multiple histone modifications revealed that SNPs in bivalent promoter/enhancer regions of adult muscle tissue significantly improved prediction accuracy across all tested densities (0.5k-15k). At 15k SNPs, accuracy improved by 26.71% (from 0.35 ± 0.02 to 0.44 ± 0.01), surpassing the maximum accuracy achievable using all SNPs in conventional methods. The method also improved predictions in distantly related populations, increasing accuracy from 0.22 ± 0.15 to 0.28 ± 0.11 at 15k SNPs. This study provides an efficient, cost-effective molecular marker screening strategy for genomic selection in aquaculture animals, advancing the practical application of genomic selection. Additionally, the cis-regulatory element annotations generated in this study offer valuable resources for functional genomics research in L. vannamei.
Keywords: genomic selection, histone modifications, SNP, Litopenaeus vannamei, epigenetics, CUT&Tag