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Current Research in Genomic Selection- Dr. Jose Santos

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Dr. Santos presented this as part of a DAIReXNET webinar. You can view the recorded webinar on YouTube at www.youtube.com/watch?v=BL1jb8WY8lk

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Current Research in Genomic Selection- Dr. Jose Santos

  1. 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
  2. 2. Milk Production per Cow in the US Milk yield (lb) Daughter Pregnancy Rate
  3. 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. 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
  5. 5. Embryos only 0 10 20 30 40 50 60 70 80 90 100 Cleaved embryos Live embryos High quality embryos *Live embryos *High quality embryos % No disease Disease P = 0.05 P < 0.01 P < 0.01 P < 0.01 P = 0.02 A 0 10 20 30 40 50 60 70 80 90 100 C em % P B 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
  6. 6. 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) < 0.001 Fever 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) 0.20 Digestive 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 6 Health Problems in the First 60 DIM and Pregnancy in Dairy Cows Santos et al. (2010) Soc. Reprod. Fertil. 67:387-403
  7. 7. Would genetic selection work? o Strong environmental effects o Low heritability (but high variation) Genetics & Fertility? 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 Milk Yield Protein 1/4 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 Conception rate Reproductive Efficiency Mastitis resistance Dairy character 1/20
  8. 8. 20 23 26 29 32 35 395 400 405 410 415 420 425 430 2003 2004 2005 2006 2007 2008 2009 2010 2011 2003 2004 2005 2006 2007 2008 2009 2010 2011 Conceptionrate,% Calvinginterval,d Year of calving or 1st breeding when lactating Calving interval Conception rate Recent Evolution of Reproductive Parameters in Holsteins Bisinotto et al. (2014) Animal 8:s1, 151–159 8
  9. 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. 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. 11. Daughter Pregnancy Rate NFH 0.2 %/yr US 0.07 %/yr Applying Intensive Genomic Selection Increases Genetic Gain Peñagaricano et al. (2016)
  12. 12. NFH 61 $/yr US 35 $/yr Lifetime Net Merit $ 231 Applying Intensive Genomic Selection Increases Genetic Gain Peñagaricano et al. (2016)
  13. 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. 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. 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. 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. 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. 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:
  19. 19. Fertility Phenotypes High-Low fertility cows Genotyping GWAS GEBV SNP-GSEA Genomic selection model for fertility Outline Extension Education
  20. 20. Thank you! jepsantos@ufl.edu http://agrilife.org/afridairycowfertility/

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