Current Research in Genomic Selection- Dr. Jose Santos
1. Genomic Selection for Improved Fertility of Dairy
Cows with Emphasis on Cyclicity and Pregnancy
P.J. Pinedo, J.E.P. Santos, W.W. Thatcher, K.N. Galvão, R.C. Bicalho,
R.O. Gilbert, G. Schuenemann, G. Rosa, S. Rodriguez-Zas S, C.
Seabury, R.C. Chebel, J. Fetrow
1
NIFA-USDA 2013-68004-20361
3. Current World Records
Smurf - 216,891 kg (478,163 pounds) over 15
years
3
Bur-Wall Buckeye Gigi 33,932 kg in 365 days
(74,650 lb; 2,126 lb fat and 2,142 lb protein)
4. Morbidity is a Problem of Early Lactation
Cows
0
20
40
60
80
100
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
Numberofcows
Day postpartum
N = 753 cows with metritis in dairy
farms in NY, OH, and CA
Metritis
Galvão et al. (2014)
0
50
100
150
200
250
300
350
400
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
Numberofcows
Week postpartum
N = 1,171 cows with non-uterine disease
(NUTD) in dairy farms in FL
Ribeiro et al. (2016) J. Dairy Sci. 99: 2201-2220
Non-uterine diseases
30 to 35% of cows are affected by disease in
the first 3 weeks of lactation
78% the first disease diagnosis occur within
3 weeks postpartum
9. Many Sires Have Improved Daughter Fertility
and Increased PTA Milk
-5.0
-4.0
-3.0
-2.0
-1.0
0.0
1.0
2.0
3.0
4.0
5.0
-1000 -500 0 500 1000 1500
DPR,PTA
Milk, PTA kg
Genomic Proven
212 bulls
milk PTA> 250 kg
DPR PTA > 1.5
Fig. 2. Milk PTA (kg) and DPR of genomic and proven sires released in
December 2011 (AIPL-USDA)
A B
C D
9
10. Phenotypic Performance: Milk vs.
Fertility
Genetic Merit: Milk vs. Fertility
Peñagaricano et al. (2016)
Phenotypic and Genetic Trends in the US
Dairy Herd
11. Daughter Pregnancy Rate
NFH 0.2 %/yr
US 0.07 %/yr
Applying Intensive Genomic Selection
Increases Genetic Gain
Peñagaricano et al. (2016)
12. NFH 61 $/yr
US 35 $/yr
Lifetime Net Merit
$ 231
Applying Intensive Genomic Selection
Increases Genetic Gain
Peñagaricano et al. (2016)
13. Productive Life
NFH 0.6
mo/yr
US 0.2 mo/yr
Applying Intensive Genomic Selection
Increases Genetic Gain
Peñagaricano et al. (2016)
14. Genomic Selection for Improved Fertility
of Dairy Cows with Emphasis on Cyclicity
and Pregnancy
NIFA-USDA 2013-68004-20361
Translational Genomics for
Improved Fertility of Animals
http://agrilife.org/afridairycowfertility/
15. 1. Develop a fertility database with genotypes and phenotypes based on direct
measures of fertility in Holstein cows
2. Identify SNPs associated with fertility traits by use of genome-wide
analyses (GWAS)
3. To obtain genomic-estimated breeding values (GEBV) that can be applied
in selection for improved fertility
4. Incorporate these findings in available platforms
5. Extend the knowledge to the dairy industry
6. Educate students on animal health, reproduction, and genetics
Objectives
Main objective is to identify molecular markers for
genomic selection to improve fertility of dairy cattle
16. Incidence (%) of diseases in the first 60 d postpartum in 11,729 dairy
cows from 16 herds according to region of the country
Region of the US
Disease SE SW MW NE Overall
Cows (farms), n 1,183 (1) 2,726 (5) 5,189 (6) 2,623 (4) 11,729 (16)
Retained placenta, % 11.3 4.0 6.3 6.9 6.4
Metritis, % 42.6 29.9 20.5 22.8 25.4
Subclinical ketosis, % 22.5 21.6 20.4 30.3 23.2
Mastitis, % 19.6 7.6 10.8 16.9 12.3
Displaced abomasum, % 5.0 0.2 2.6 2.0 2.2
Clinical endometritis, % 32.9 26.4 24.4 24.0 25.7
Lameness, % 12.5 9.3 13.9 10.7 11.9
Death, % 2.2 1.3 2.6 1.6 2.0
Morbidity, % 61.0 42.9 40.7 41.2 43.4
Pinedo et al. (2016) J. Dairy Sci. Abstr.
~45% of the dairy cows are diagnosed with a
problem in the first 60 DIM
17. Subpopulations for extreme high and low fertility:
High-fertility cows (n=850): Pregnant cows on d 60 after first AI
with the highest RI
Low-fertility cows (n=1,750): Non-pregnant cows on d 60 after
two postpartum AI with the lowest RI
Approach
Genotyping:
0.00
0.20
0.40
0.60
0.80
1.00
A B C D E F G H I J K L
High
Low
18. New pool of 1,000 cows based on high and low RI and a
group of 200 AI sires with extreme values for daughter
fertility (high DPR > +1.5 vs. low DPR < -1.5).
Approach
Validation:
33,962 - Smurf produced this milk in 11 lactations from what I read. She was retired to pasture for a couple of years before she was euthanized and died at age 15-16.