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

• 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.

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

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

BREEDING PROGRAM
Progeny
test
type
classification
milk testRegistration
Genetic
evaluation

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

Breed composition evaluation
• Morphological characters
– coat color, horn shape, stature ,
humped/humpless, ...
• Genetic makers
– microsatellite
– dense SNPs
– whole genome sequences?
• in near future

Microsatellite makers: a case study on
Asian buffalo

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

Distribution of domestic buffalo
swampriver
World 195 million ~81% ~19%

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

Genetic differentiation of Chinese buffalo
20 swamp, 2 river
1355 individuals

64 samples / gel
Genotyping by ABI sequencer
GENESCAN ® 2.0

Genetic composition of Chinese buffalo
STRUCTURE 2.0 (Pritchard et al., 2000)

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

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

Dense SNP markers: a case study of Chinese
local cattle breeds
Primary results (unpublished)

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)

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

Sampling localities
MG2
MG1
YB
LX
NY
QC
KZK
TBT
DH DC
BGD
EH WN WL

延边牛
南阳牛

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

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.

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.

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.

NJ tree
China(N)China(C)
China(SW) China(S)
China(C)

NJ tree: population-based
The distance is used the Reynold distance

Advantages of dense SNP markers
• More informative for breed composition
evaluation
• Individual animal based analysis
• Ready for cross-lab combined analysis

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)