The objectives of this study were to estimate genetic parameters of lactation average somatic cell scores (LSCS) and examine genetic associations between LSCS and production traits in the first three lactations of Chinese Holstein cows using single-parity multi-trait animal model and multi-trait repeatability animal model. There were totally 273 605 lactation records of Chinese Holstein cows with first calving from 2001 to 2012. Heritability estimates for LSCS ranged from 0.144 to 0.187. Genetic correlations between LSCS and 305 days milk, protein percentage and fat percentage were –0.079, –0.082 and –0.135, respectively. Phenotypic correlation between LSCS and 305 days milk yield was negative (–0.103 to –0.190). Genetic correlation between 305 days milk and fat percentage or protein percentage was highly negative. Genetic correlation between milk fat percentage and milk protein percentage was highly favorable. Heritabilities of production traits decreased with increase of parity, whereas heritability of LSCS increased with increase of parity.

Our previous studies demonstrated that the region around markers BMS470 and BMS1242 on BTA6 showed a linkage to 305-d milk yield and composition traits in the Chinese Holstein population. We herein focused on such narrow region to fine map milk production QTLs with 15 SNPs across 25 Mb with each SNP in 1 Mb within most regions in a Chinese Holstein population with daughter design. 1 449 Holstein cows and 11 sires were genotyped for such SNPs by using TaqMan probe and RFLP assays. Multipoint linkage analysis across family revealed a QTL affecting milk yield between PPARGC1A C4075T and SLC34A2 T1713C. Meanwhile, within family analysis found three milk yield QTLs (two in CR T60984131G-CEP135 C501T and one in PDLIM5 A106C-OPN T3907, a fat yield QTL in UGDH T1670C-CR T60984131G region, and two protein yield QTLs in TBC1D1 G501C-UGDH T1670C and PPARGC1A C4075T-SLC34A2 T1713C, respectively. Associations between aforementioned significant SNP markers and milk production traits were further implemented. We found significant associations of PPARGC1A C4075T, SLC34A2 T1713C with milk yield (P<0.05, P<0.01, P<0.01), UGDH T1670C, and CR T60984131G with fat yield (P<0.01, P<0.01), and PPARGC1A C4075T, SLC34A2 T1713C, UGDH T1670C and OPN T3907 with protein yield (P<0.01, P<0.01, P<0.01, P<0.01). Our findings implied that QTLs affecting milk production traits on BTA6 were pleictropism or multigenic effect and PPARGC1A and OPN may be the causal mutations behind milk production QTLs on BTA6 in the Chinese Holstein population.

Current study adopted gene flow theory and selection index method to compare the breeding efficiency of three breeding plans in the Chinese Holstein cattle using ZPLAN software. Simulated conventional progeny-testing program (PT) and young sire program (YS) were compared with breeding program using genomic selection (GS) taking parameters derived from Chinese Holstein breeding system. The results showed that, GS shortened generation interval by 1.5-2.2 years, and increased the genetic progress by 30-50%, comparing to PT and YS, respectively. Economic analysis showed that GS could obtain a higher breeding efficiency, being 119 and 97% higher than that of PT and YS, respectively; and GS was also powerful in improving functional traits with a low heritability. Main factors affecting breeding efficiency in GS were further discussed, including selection intensity, accuracy and the cost of SNP genotyping. Our finding provided references for future designing and implementing GS in Chinese dairy population.