Genomic Dissection of Growth Traits and Spatial Independence from Breed-Defining Loci in Jining Grey Goats

Improving growth while preserving breed-defining characteristics is a central challenge in indigenous livestock breeding. We addressed this issue in Jining Grey goats using low-depth whole-genome sequencing and a conservative multi-evidence marker-prioritization framework. The discovery cohort included 70 performance-graded goats at 3 months (n = 37) and 6 months (n = 33; mean depth, 2.07×), and 47 seven-day-old goats from the same project were used for exploratory early-life trend analysis (mean depth, 2.10×). After site-level filtering, phasing, and within-cohort imputation, masking-based assessment of 120,000 genotype cells yielded 94.38% exact genotype concordance and a hard-dosage correlation of 0.919. Performance grading captured consistent differences in body weight and body-size traits, but the small 3-month Conventional group required conservative interpretation. Selective-sweep analyses highlighted breed-background regions, including signals near KIT, whereas GWAS and superior-genotype comparisons prioritized candidate growth loci, including chr10:78518687 for six-month chest girth and literature-supported genes involved in muscle growth and developmental regulation. Overlap and permutation analyses indicated limited physical overlap between growth-prioritized loci and major selective-sweep regions. A 99-SNP candidate panel showed exploratory prediction potential (maximum cross-validated r ≈ 0.47), whereas seven-day analyses showed only nominal trends without FDR significance. These findings provide a preliminary marker resource for future Jining Grey goat breeding and conservation, pending external validation, denser genotyping, and functional confirmation.