Current Research in Genomic Selection- Dr. Jose Santos
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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
Transcript of Current Research in Genomic Selection- Dr. Jose Santos
Genomic Selection for Improved Fertility of Dairy Cows with Emphasis on Cyclicity and PregnancyP.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
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NIFA-USDA 2013-68004-20361
Milk Production per Cow in the US
Milk yield (lb) Daughter Pregnancy Rate
Current World Records
Smurf - 216,891 kg (478,163 pounds) over 15 years
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Bur-Wall Buckeye Gigi 33,932 kg in 365 days(74,650 lb; 2,126 lb fat and 2,142 lb protein)
Morbidity is a Problem of Early Lactation Cows
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 210
20406080
100
Day postpartum
Num
ber o
f cow
s N = 753 cows with metritis in dairy farms in NY, OH, and CA
Metritis
Galvão et al. (2014)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 240
50100150200250300350400
Week postpartum
Num
ber o
f cow
s
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 diseases30 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
Embryos only
0
10
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30
40
50
60
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Cleavedembryos
Liveembryos
Highquality
embryos
*Liveembryos
*Highquality
embryos
%
No disease Disease
P = 0.05 P < 0.01 P < 0.01 P < 0.01 P = 0.02
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Cleavedembryos
Liveembryos
Highquality
embryos
*Liveembryos
*Highquality
embryos
%
No UTD UTD
P = 0.02 P < 0.01 P < 0.01 P < 0.01 P = 0.03
B
0
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Cleavedembryos
Liveembryos
Highquality
embryos
*Liveembryos
*Highquality
embryos
%
No NUTD NUTD
P = 0.63 P = 0.05 P = 0.05 P = 0.03 P = 0.05
C
Ova-embryos
Disease Influences Development to Morula
Ribeiro et al. (2016) J. Dairy Sci. 99:2201–2220
419 embryo-oocytes from single ovulating lactating Holstein cows
Category Pregnant, % Adjusted OR (95% CI) P
Healthy 51.4 1.00
1 case of disease 43.3 0.79 (0.69 – 0.91) 0.001
> 1 case of disease 34.7 0.57 (0.48 – 0.69) < 0.001
Type of health problem
Calving problem 40.3 0.75 (0.63 – 0.88) < 0.001
Metritis 37.8 0.66 (0.56 – 0.78) < 0.001
Clinical endometritis 38.7 0.62 (0.52 – 0.74) < 0.001Fever postpartum 39.8 0.60 (0.48 – 0.65) < 0.001
Mastitis 39.4 0.84 (0.64 – 1.10) 0.20
Clinical ketosis 28.8 0.50 (0.36 – 0.68) < 0.001
Lameness 33.3 0.57 (0.41 – 0.78) < 0.001
Pneumonia 32.4 0.63 (0.32 – 1.27) 0.20Digestive problem 36.7 0.78 (0.46 – 1.34) 0.38
5,719 postpartum dairy cows evaluated daily for health disorders in seven dairy farms in the US
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Health Problems in the First 60 DIM and Pregnancy in Dairy Cows
Santos et al. (2010) Soc. Reprod. Fertil. 67:387-403
Would genetic selection work?
o Strong environmental effectso Low heritability (but high variation)
Genetics & Fertility?
Milk YieldMilk fatProtein
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4
1/4
Conception rateReproductive Efficiency
Mastitis resistanceDairy character
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4
1/20
200320042005200620072008200920102011200320042005200620072008200920102011
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35Calving interval Conception rate
Year of calving or 1st breeding when lactating
Cal
ving
inte
rval
, dC
onception rate, %Recent Evolution of Reproductive Parameters
in Holsteins
Bisinotto et al. (2014) Animal 8:s1, 151–1598
Many Sires Have Improved Daughter Fertility and Increased PTA Milk
-5.0-4.0-3.0-2.0-1.00.01.02.03.04.05.0
-1000 -500 0 500 1000 1500
DPR
, PTA
Milk, PTA kg
Genomic Proven212 bullsmilk PTA> 250 kgDPR PTA > 1.5
Fig. 2. Milk PTA (kg) and DPR of genomic and proven sires released inDecember 2011 (AIPL-USDA)
A B
C D
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Phenotypic Performance: Milk vs. Fertility
Genetic Merit: Milk vs. Fertility
Peñagaricano et al. (2016)
Phenotypic and Genetic Trends in the US Dairy Herd
Daughter Pregnancy Rate
NFH 0.2 %/yr
US 0.07 %/yr
Applying Intensive Genomic Selection Increases Genetic Gain
Peñagaricano et al. (2016)
NFH 61 $/yr
US 35 $/yr
Lifetime Net Merit
$ 231
Applying Intensive Genomic Selection Increases Genetic Gain
Peñagaricano et al. (2016)
Productive Life
NFH 0.6
mo/yr
US 0.2 mo/yr
Applying Intensive Genomic Selection Increases Genetic Gain
Peñagaricano et al. (2016)
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/
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
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
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
ApproachGenotyping:
A B C D E F G H I J K L0.000.100.200.300.400.500.600.700.800.901.00
High Low
n = 2,600
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).
ApproachValidation:
Fertility Phenoty
pes
High-Low fertility cows
Genotyping GWAS GEBV SNP-
GSEA
Genomic selection model for
fertility
Outline
Extension
Education
