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Fine Mapping QTLs Affecting Milk Production Traits on BTA6 in chinese holstein with SNP Markers

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Journal of Integrative Agriculture 2013年第1期12卷 110-117页

作者： LIU Rui SUN Dong-xiao WANG Ya-chun YU Ying ZHANG Yi CHEN Hui-yong ZHANG Qin ZHANG Sheng-li ZHANG Yuan College of Animal Science and Technology/Key Laboratory of Animal Genetics and Breeding Ministry of Agriculture/National Engineering Laboratory of Animal Genetics/China Agricultural University Sichuan Animal Science Academy

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 QTLin 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 （P0.05, P0.01, P0.01）, UGDH T1670C, and CR T60984131G with fat yield （P0.01, P0.01）, and PPARGC1A C4075T, SLC34A2 T1713C, UGDH T1670C and OPN T3907 with protein yield （P0.01, P0.01, P0.01, P0.01）. 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.

关键词： fine mapping milk production trait SNP BTA6 chinese holstein

Genetic parameters for somatic cell score and production traits in the fi rst three lactations of chinese holstein cows

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Journal of Integrative Agriculture 2015年第1期14卷 125-130页

作者： ZHAO Fu-ping GUO Gang WANG Ya-chun GUO Xiang-yu ZHANG Yuan DU Li-xin National Center for Molecular Genetics and Breeding of Animal Institute of Animal SciencesChinese Academy of Agricultural Sciences Beijing Sanyuan Dairy Cattle Breeding Center College of Animal Science and Technology China Agricultural University

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 273605 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.

关键词： somatic cell score genetic parameters chinese holstein single-parity multi-trait animal model multi-traitrepeatability animal model

Evaluation of Breeding Programs Combining Genomic Information in chinese holstein

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Agricultural Sciences in China 2011年第12期10卷 1949-1957页

作者： CHEN Jun WANG Ya-chun ZHANG Yi SUN Dong-xiao ZHANG Sheng-li ZHANG Yuan College of Animal Science and Technology/National Engineering Laboratory for Animal Breeding/Key Laboratory of Agricultural Animal Genetics and Breeding China Agricultural University Beijing 100193 P.R.China

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.

关键词： chinese holstein genomic selection progeny-testing program young sire program breeding plan

Comparison of Estimated Genetic Connectedness among Three Herds of chinese holstein Cattle

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Journal of Animal Science and Biotechnology 2010年第3期1卷 133-136页

作者： Jun Chen YachunWang Yi Zhang Yuan Zhang College of Animal Science and Technology Key Laboratory of Ministry of Agriculture China Agricultural University Beijing 100193 China

Estimating genetic connectedness among herds is important for the accuracy of dairy cattle genetic evaluation. When selecting between animals raised in different herds, the accuracy of their genetic evaluations can be influenced by the degree of connectedness among these herds. In this study, two methods were used to measure genetic connectedness, CR （genetic connectedness rating ） and GLt （total number of direct genetic links between group）, among herds from Beijing, Shanghai, and Tianjin. Genetic connectedness between the herds from Beijing and Tianjin was 23.95%, between Beijing and Shanghai was 17. 10%, and between Shanghai and Tianjin it was 14.28%. Genetic connectedness between herds from Beijing and Tianjin was the highest and that between Shanghai and Tianjin was the lowest. The correlation coefficient for the two methods was 0. 808. Some suggestions for improved genetic evaluation of dairy cattle were also discussed.

关键词： cattle chinese holstein genetic connectedness genetic evaluation

A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

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Journal of Animal Science and Biotechnology 2021年第1期12卷 122-140页

作者： Lijun Shi Xin Wu Yuze Yang Zhu Ma Xiaoqing Lv Lin Liu Yanhua Li Feng Zhao Bo Han Dongxiao Sun Department of Animal Genetics Breeding and ReproductionCollege of Animal Science and TechnologyKey Laboratory of Animal GeneticsBreeding and Reproduction of Ministry of Agriculture and Rural AffairsNational Engineering Laboratory for Animal BreedingChina Agricultural UniversityNo.2 Yuanmingyuan West RoadHaidian DistrictBeijing 100193China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China Beijing General Station of Animal Husbandry Beijing 100101China Beijing Dairy Cattle Center Beijing 100192China.

Background: People are paying more attention to the healthy and balanced diet with the improvement of their living standards. Milk fatty acids(FAs) have been reported that they were related to some atherosclerosis and coronary heart diseases in human. In our previous genome-wide association study(GWAS) on milk FAs in dairy cattle, 83 genomewide significant single nucleotide polymorphisms(SNPs) were detected. Among them, two SNPs, ARS-BFGL-NGS-109493 and BTA-56389-no-rs associated with C18 index(P = 0.0459), were located in the upstream of 1-acylglycerol-3-phosphate O-acyltransferase 3(AGPAT3) gene. AGPAT3 is involved in glycerol-lipid, glycerol-phospholipid metabolism and phospholipase D signaling pathways. Hence, it was inferred as a candidate gene for milk FAs. The aim of this study was to further confirm the genetic effects of the AGPAT3 gene on milk FA traits in dairy cattle.Results: Through re-sequencing the complete coding region, and 3000 bp of 5′ and 3′ regulatory regions of the AGPA T3 gene, a total of 17 SNPs were identified, including four in 5′ regulatory region, one in 5′ untranslated region(UTR),three in introns, one in 3′ UTR, and eight in 3′ regulatory region. By the linkage disequilibrium(LD) analysis with Haploview4.1 software, two haplotype blocks were observed that were formed by four and 12 identified SNPs,respectively. Using SAS9.2, we performed single locus-based and haplotype-based association analysis on 24 milk FAs in 1065 chinese holstein cows, and discovered that all the SNPs and the haplotype blocks were significantly associated with C6:0, C8:0 and C10:0(P A, g.146704373 A > G, g.146704618 A > G and g.146704699 G > A) changed the transcription factor binding sites(TFBSs) for transcription factors SMARCA3, REX1, VMYB, BRACH, NKX26, ZBED4, SP1, USF1, ARNT and FOXA1. Out of them, two SNPs were validated to impact transcriptional activity by performing luciferase assay that the a

关键词： AGPAT3 chinese holstein Genetic effects Milk fatty acids Potential causal mutation

A post-GWAS replication study confirming the association of C14H8orf33 gene with milk production traits in dairy cattle

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Frontiers of Agricultural Science and Engineering 2014年第4期1卷 321-330页

作者： Shaohua YANG Chao QI Yan XIE Xiaogang CUI Yahui GAO Jianping JIANG Li JIANG Shengli ZHANG Qin ZHANG Dongxiao SUN Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture National Engineering Laboratory of Animal BreedingCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Genome-wide association studies with an Illumina Bovine50K chip have detected 105 SNPs associated with one or multiple milk production traits in the chinese holstein population.Of these,38 significant SNPs detected with high confidence by both L1-TDT and MMRA methods were selected to further mine potential key genes affecting milk yield and milk composition.By blasting the flanking sequences of these 38 SNPs with the bovine genome sequence combined with comparative genomics analysis,26 genes were found to contain or be near to such SNPs.Among them,the C14H8orf33 gene is merely 87 bp away from the significant SNP,Hapmap30383-BTC-005848.Hence,we report herein genotype-phenotype associations to further validate the genetic effects of the C14H8orf33 gene.By pooled DNA sequencing of 14 unrelated holstein sires,a total of 18 with seven novel SNPs were identified.Among them,nine SNPs were in the 5′regulatory region,one in exon 6 and the other in the 3′UTR and 3′regulatory region.A total of nine of these identified SNPs were successfully genotyped and analyzed by mass spectrometry for association with five milk production traits in an independent resource population.The results showed that these SNPs were statistically significant for more than two traits[Pchinese holstein breeding programs.

关键词： GWAS functional annotation chinese holstein milk production traits C14H8orf33 gene single nucleotide polymorphisms association study

The Bovine CXCR1 Polymorphisms Not Associated with Somatic Cell Score and Milk Traits in Dairy Cattle

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The Bovine CXCR1 Polymorphisms Not Associated with Somatic C...