implementation of genomic selection in uk dairy goats · 2021. 3. 2. · goat milk •increasing...
TRANSCRIPT
![Page 1: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/1.jpg)
Leading the way in Agriculture and Rural Research, Education and Consulting
Implementation of genomic selection in UK dairy goats
Mucha S., Desire S., Mrode R., Coffey M., Conington J.email: [email protected]
EAAP, 29th August 2016
1
![Page 2: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/2.jpg)
Goat milk
• Increasing popularity of goat milk• 90,000 dairy goats
– 1/3 on few large commercial farms• Produce majority of milk
– Small scale industry - ‘Niche’ market
2
![Page 3: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/3.jpg)
Breeding value• Routine breeding value estimation
– France, Canada, US, Norway, UK• Genomic breeding values
– France, UK
• Specific structure of reference population– Low number of animals– Mixture of males and females– Limited exchange of genotypes
3
![Page 4: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/4.jpg)
Goat genomics
• 50K SNP caprine chip – Introduced in December 2011– 12000 chips sold world-wide
• 7000 in UK
4
![Page 5: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/5.jpg)
Breed composition• Crossbred goat population
– Saanen– Toggenburg– Alpine
http://www.allgoats.com
http://www.allgoats.com
http://www.allgoats.com 5
![Page 6: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/6.jpg)
Population stratification
6
![Page 7: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/7.jpg)
Animals
• 2 dairy goat farms
• 19,790 goats
• Lactation 1 – 6
• Years 1987 – 2016
7
![Page 8: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/8.jpg)
Pedigree
• 38,273 individuals
• 16 generations
• 2,799 founders
• 386 sires & 16,112 dams
8
![Page 9: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/9.jpg)
Phenotypes
• 1,337,653 milk yield records• 123,611 milk composition records
– 11,741 goats• 6,723 conformation scores• 11,844 mastitis records
9
![Page 10: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/10.jpg)
Initial genotyped population
• Training: 1,474 1,410 ♀ & 64 ♂
• Validation: 305 302 ♀ & 3 ♂
• Young : 123 56 ♀ & 67 ♂
• TOTAL: 1,902
• Illumina Caprine 50K BeadChip• 47,306 SNP after QA
10
![Page 11: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/11.jpg)
Current genotyped population
• Training: 3,793 3,675 ♀ 118 ♂
• Validation: 1,419 1,407♀ 12♂
• Young : 3,764 3,521♀ 243♂
• TOTAL: 8,976
• Illumina Caprine 50K BeadChip• 44,670 SNP after QA
11
![Page 12: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/12.jpg)
Accuracy of milk yd GEBVs
0
0,25
0,5
0,75
1
PBLUP HBLUP
0.58 0.61
12
![Page 13: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/13.jpg)
Accuracy
13
0
0,2
0,4
0,6
0,8
1
FATyd PROTyd LACTyd
0.50 0.53 0.46
![Page 14: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/14.jpg)
Conformation scoring
• 9 traits• Linear scale (1 – 9)• Similar to CAPGENES• 2 scorers
14
![Page 15: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/15.jpg)
Conformation traits
15
![Page 16: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/16.jpg)
Heritability
0.28 0.38 0.15 0.32 0.36 0.23 0.02 0.13 0.13 0.24
16
![Page 17: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/17.jpg)
Genotyped population
0
500
1000
1500
2000
2500
UF UD UA TS TA TP BL FF BF
TrainingValidation
17
![Page 18: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/18.jpg)
Accuracy
0.23 0.39 0.26 0.18 0.39 0.48 0.21 0.55 0.04
18
![Page 19: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/19.jpg)
Sub-clinical & clinical mastitis
• Frequency: 4.96%• Heritability: 0.05 ± 0.01 • Accuracy: 0.30
19
![Page 20: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/20.jpg)
Future plans
• Genomics of new traits– Out of season breeding– Longevity– Feed efficiency– Parentage panel– Sequence analysis– ...
20
![Page 21: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/21.jpg)
Acknowledgement
21
![Page 22: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/22.jpg)
Thank you for your attention
22
![Page 23: Implementation of genomic selection in UK dairy goats · 2021. 3. 2. · Goat milk •Increasing popularity of goat milk •90,000 dairy goats –1/3on few large commercial farms](https://reader035.vdocuments.us/reader035/viewer/2022081621/6133a1e7dfd10f4dd73b36d0/html5/thumbnails/23.jpg)
Leading the way in Agriculture and Rural Research, Education and Consulting