breed composition evaluation based on genetic makers
DESCRIPTION
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 2014TRANSCRIPT
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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
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• 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.
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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
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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
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BREEDING PROGRAM
Progeny test
type classification
milk test Registration
Genetic evaluation
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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
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Breed composition evaluation
• Morphological characters
– coat color, horn shape, stature , humped/humpless, ...
• Genetic makers
– microsatellite
– dense SNPs
– whole genome sequences?
• in near future
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Microsatellite makers: a case study on Asian buffalo
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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
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Distribution of domestic buffalo
swamp river
World 195 million ~81% ~19%
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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
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Genetic differentiation of Chinese buffalo
20 swamp, 2 river
1355 individuals
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64 samples / gel
Genotyping by ABI sequencer
GENESCAN ® 2.0
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Genetic composition of Chinese buffalo
STRUCTURE 2.0 (Pritchard et al., 2000)
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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 NL XF
Upper and Middle
Reaches of Yangtze Lower Reaches
of Yangtze
South-China Southwest of
China
River
buffalo
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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
7873
85
58
97
1
2
3
4
(1)
(2)
(3)
(4) Clustering tree of 17 Swamp
without Dehong
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Dense SNP markers: a case study of Chinese local cattle breeds
Primary results (unpublished)
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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)
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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
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Sampling localities
MG2
MG1
YB
LX
NY QC
KZK
TBT
DH DC
BGD
EH WN WL
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延边牛
南阳牛
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355 individuals from 14 populations genotyped on Illumina BovineSNP50
54609 autosomal SNPS
Call rates ≥ 90% 828 SNPs
5897 SNPs MAF ≥ 0.01
8 individuals missingness≤90%
347 individuals 43823 SNPs
347 individuals from 14 populations 43823 autosomal SNPs
4597 SNPs HWE ≥ 1e-006
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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.
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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.
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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.
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NJ tree
China(N) China(C)
China(SW) China(S)
China(C)
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NJ tree: population-based
The distance is used the Reynold distance
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Advantages of dense SNP markers
• More informative for breed composition evaluation
• Individual animal based analysis
• Ready for cross-lab combined analysis
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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)