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 test Registration

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

swamp river

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 NL XF

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

7873

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 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

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)