Breed composition evaluation based on genetic makers

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Presented by Yi Zhang (College of Animal Science and Technology, China Agricultural University, Beijing) at the Inception workshop of the AgriTT project: Evaluation of breed composition, productivity and fitness for smallholder dairy cattle in Tanzania, Dar es Salaam, 10-11 June 2014

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Breed composition evaluation based on genetic makers

  1. 1. Breed composition evaluation based on genetic makers Yi Zhang College of Animal Science and Technology China Agricultural University, Beijing Inception workshop of the AgriTT project: Evaluation of breed composition, productivity and fitness for smallholder dairy cattle in Tanzania, Dar es Salaam, 10-11 June 2014
  2. 2. • CAU was formed by merging Beijing Agricultural University and Beijing Agricultural Engineering University in 1995 • The earliest agricultural school in China, dated back to 1905 • About 60,000 students are currently enrolled.
  3. 3. College of Animal Science & Technology • Departments – Animal Genetics, Breeding & Reproduction – Animal Nutrition & Feed Science – Forage & Grassland Science • Students – Bachelor degree • ~120 students per year – Master degree • ~95 students per year – Doctor degree • ~25 students per year
  4. 4. Dairy genetics and breeding group • 5 faculty members • 14 graduate students, 10 PhD students • Research areas – Genetic characterization of Chinese bovine breeds – Genomic selection of Holstein cattle – Genome-wide association for gene mapping – Genetic recessive defect and selective mating – Genetic improvement of Chinese local cattle breed • Sanhe cattle
  5. 5. BREEDING PROGRAM Progeny test type classification milk testRegistration Genetic evaluation
  6. 6. Why we are interested in the type of breed? • Natural vs. artificial selection • Selective breeding in livestock species is successful – for particular traits of interest – genetic type for specific uses • beef cattle, dairy cattle • layer, broiler chicken • wool, meat, dairy sheep • There is no breed fitting all production systems
  7. 7. Breed composition evaluation • Morphological characters – coat color, horn shape, stature , humped/humpless, ... • Genetic makers – microsatellite – dense SNPs – whole genome sequences? • in near future
  8. 8. Microsatellite makers: a case study on Asian buffalo
  9. 9. swamp type Classification of domestic buffalo river type Chr 4 of River Chr 9 of River Chr 9 of Swamp Chr 4 of River Chr 9 of River Chr 9 of Swamp1 Chr 4 of River Chr 9 of River Chr 9 of Swamp Chr 4 of River Chr 9 of River Chr 9 of Swamp1 2n =48 2n = 50
  10. 10. Distribution of domestic buffalo swampriver World 195 million ~81% ~19%
  11. 11. Swamp buffalo resources: current status Primarily employed as a work animal for crop production, not subject to breeding programs  37.3 million, widely distributed in South of China (63%) and Southeast Asia (37%) but no breed recognized terrace
  12. 12. Genetic differentiation of Chinese buffalo 20 swamp, 2 river 1355 individuals
  13. 13. 64 samples / gel Genotyping by ABI sequencer GENESCAN ® 2.0
  14. 14. Genetic composition of Chinese buffalo STRUCTURE 2.0 (Pritchard et al., 2000)
  15. 15. GB GZ FL YJ ES JH HZ SQ DL XJ FA XG FZ XL DC DD K=2 STRUCTURE analysis K=5 K=4 K=3 K=6 DH MR NLXF Upper and Middle Reaches of Yangtze Lower Reaches of Yangtze South-China Southwest of China River buffalo
  16. 16. GZ GB YJ NS FL JH SQ HZ DL XJ FA XF FZ L XL DD DC 87 58 81 78 43 28 50 41 38 78 73 85 58 97 1 2 3 4 (1) (2) (3) (4) Clustering tree of 17 Swamp without Dehong
  17. 17. Dense SNP markers: a case study of Chinese local cattle breeds Primary results (unpublished)
  18. 18. Illumina Bovine BeadChip  Illumina Bovine3k BeadChip (2,900 SNPs)  Illumina BovineLD BeadChip (6,909 SNPs)  Illumina Infinium BovineLD v1.1 BeadChip (6912 SNPs)  Illumina BovineSNP50v1 BeadChip (54,001 SNPs)  Illumina BovineSNP50v2 BeadChip (54,609 SNPs)  Illumina BovineHD BeadChip (777,962 SNPs)
  19. 19. Analysis of population structure Quality Control (using PLINK) call rate, missingness, Hardy-Weignberg equilibrium Data analysis Structure analysis Principal component analysis (PCA) Neighbor-Joining trees construction
  20. 20. Sampling localities MG2 MG1 YB LX NY QC KZK TBT DH DC BGD EH WN WL
  21. 21. 延边牛 南阳牛
  22. 22. 355 individuals from 14 populations genotyped on Illumina BovineSNP50 54609 autosomal SNPS Call rates ≥ 90% 828 SNPs 5897 SNPsMAF ≥ 0.01 8 individuals missingness≤90% 347 individuals 43823 SNPs 347 individuals from 14 populations 43823 autosomal SNPs 4597 SNPsHWE ≥ 1e-006
  23. 23. Structure analysis MG2 is sampled from a region where crossbreeding between local breed and European breeds (esp. Holstein, Simmental) is popular. KZK is sampled from a region where Brown Swiss is usually used in crossbreeding.
  24. 24. PCA plot: individual-based The 1st component, accounting for 11.74% of variation, corresponds to a northern/southern (taurus/indicus) gradient and the 2nd component, accounting for 1.96% of variation, reflects differentiation within Northern taurine cattle.
  25. 25. PCA, population-based The 1st component accounting for 74.8% of variation corresponds to a northern/southern (taurus/indicus) gradient, and the 2nd component accounting for 17.5% of variation, however, can not be easily interpreted.
  26. 26. NJ tree China(N)China(C) China(SW) China(S) China(C)
  27. 27. NJ tree: population-based The distance is used the Reynold distance
  28. 28. Advantages of dense SNP markers • More informative for breed composition evaluation • Individual animal based analysis • Ready for cross-lab combined analysis
  29. 29. Tanzania Dairy Genetics Project • Evaluation of genetic type of breed – Field records are most important – Experimental design and sample selection – Detailed information for each sample • morphological traits • production, reproduction, disease records, – Genotyping methods • Commercially available SNP chip • Customized SNP chip • GBS (Genotyping by Sequencing)

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