Application of the “Yuyang Muxin” Breeding Chip in Huang-Huai Sheep: A Six-Year Comprehensive Evaluation of Production and Meat Quality Traits

The Huang-huai sheep (Dorper × Small-tailed Han), certified in China in 2019, initially exhibited issues with genetic uniformity and meat quality. A six-year (2020-2025) breeding program was conducted at two core farms (collectively housing ~2400 breeding ewes representing 12 bloodlines) using the custom "Yuyang Muxin" 10 K SNP chip containing functional markers for reproduction (<i>FecB</i>), growth (<i>CLPG</i>, <i>ACTC1</i>), and meat quality (<i>FABP3</i>, <i>CIDEa</i>). Genotyping and marker-assisted selection were integrated with BLUP breeding values. After six years, favorable <i>FecB</i> genotype frequency increased from 68.97% to 82.58% (<i>p</i> < 0.05), while genetic diversity remained stable (F_IS < 0.05). Mixed model analysis accounting for farm and year random effects revealed significant genetic gains: 6-month ram body weight increased by 9.1% (58.50 to 63.80 kg, <i>p</i> < 0.05), dressing percentage improved from 56.02% to 57.8% (<i>p</i> < 0.05), and loin muscle area expanded by 9.4% (24.50 to 26.8 cm², <i>p</i> < 0.05). Meat quality was enhanced, with shear force decreasing by 14.1% (38.65 to 33.20 N, <i>p</i> < 0.05) and intramuscular fat increasing by 40.0% (2.0% to 2.8%, <i>p</i> < 0.05). Lambs weaned per ewe per year increased from 2.38 to 2.56 (<i>p</i> < 0.05). EBV trend analysis confirmed that improvements were primarily genetic. After Bonferroni correction, <i>CIDEa</i> expression was strongly correlated with intramuscular fat (<i>r</i> = 0.89, <i>p</i> < 0.001) and <i>FABP3</i> expression with arachidonic acid (<i>r</i> = 0.70, <i>p</i> < 0.001). Nine months was identified as the optimal slaughter age. The "Yuyang Muxin" breeding chip effectively accelerated genetic improvement in Huang-huai sheep, enabling synergistic enhancement of multiple traits.