Development and Applications of a 1K SNP Panel for Whiteleg Shrimp: From Pedigree Reconstruction to Genomic Selection

Litopenaeus vannamei, the most widely farmed crustacean, relies on family-based selection where accurate pedigree information is essential. Although SNP-based tools offer high-accuracy pedigree assignment, adoption in commercial breeding remains limited. In this study, we developed a commercially viable 1K SNP panel with 1125 markers. Markers were selected from a 55K SNP dataset comprising 2330 individuals. We established a practical pedigree reconstruction workflow and implemented the panel in a field breeding population. The population included a selection group where families were reared separately and a test group where individuals were communally reared. We introduced anchor individuals from the selection group to enable pedigree linkage. All 1818 individuals from 72 families were accurately assigned. Family reconstruction achieved 100% consistency with known records, even when parents were partially missing. Heritability estimates for harvest weight ranged from 0.32 to 0.36 using pedigree-based BLUP (PBLUP), genomic BLUP (GBLUP), and single-step genomic BLUP (ssGBLUP). The ssGBLUP model, using a 0.15 to 0.85 weighting of G and A, achieved 6.67% and 19.40% higher accuracy than PBLUP and GBLUP. The panel also supported population structure analysis and diversity monitoring, demonstrating its value for genomic evaluation in commercial L. vannamei breeding.