1. Detection of QTL in beef cattle Eduardo Casas U.S. Meat Animal Research Center, Clay Center, Nebraska

2. Cell Chromosome Nucleosome Double helix Sequence DNA structure

3. Microsatellites and Single Nucleotide Polymorphisms Alelle A Alelle B CCGTATCACACAGTCAAC CCGTATCACACACACAGTCAAC GAACTAGCTTGAC GAACTGGCTTGAC Microsatellites SNP

4. Dam 1234581011 Microsatellites Sire allele 1 Sire allele 2 Dam allele 1 Dam allele 2 Sire

5. (Kappes et al., 1997) Bovine Chromosome 2 (BTA2).

8. BOVINE CHROMOSOME 5 Quantitative trait loci (QTL) on bovine chromosome 5

9. Identification of QTL in cattle What have we used to identify QTL? What have we found? Where are we validating them?

10. Family from sire 921467 (BM) X X n= 245 BM

11. Family from sire 921690 (PA) X X n= 209 PA

12. X X n= 500 Family from 906802 (Bonzo)

13. X X n= 500 Family from 906801 (Blackie)

14. http://www.ansi.okstate.edu/breeds/index.htm ¼ Hereford ¼ Angus ¼ Pinzgauer ¼ Red Poll MARC III

15. Traits measured Growth traits: - Birth weight (kg). - Weaning weight (kg). - Yearling weight (kg). - Postweaning average daily gain (kg/d). daily gain (kg/d). Measured carcass traits: - Hot carcass weight (kg). - Fat depth (cm). - Marbling score. - Longissimus muscle area (cm 2 ). - USDA yield grade. -Est. kidney, pelvic, & heart fat (%). -Rib bone. -Ribfat. - Ribmus. - Warner-Bratzler shear force 2 or 3 d postmortem (kg). - Warner-Bratzler shear force 14 d postmortem (kg). Predicted carcass traits: - Retail product yield (%). - Fat yield (%). - Bone yield (%). - Dressing percent (%).

16. Identification of QTL in cattle What have we used to identify QTL? What have we found? Where are we validating them?

17. Blackie Bonzo GENOME SCAN RESULTS IN ALL RESOURCE FAMILIES BTA2 MSTN BTA1 RPYD FATYD MARB, RPYD MARB BTA3 MARB, RPYD Fat yield BTA4 RPYD, FATYDWBS14 HCW, WBS3 BTA5 FAT, YG, RPYD, WBS14 RIBBONE, DP, RIBFAT, BWT BTA8 FAT, MARB FAT BTA15 WBS14 BTA27 MARB Dairy Form BTA29 WBS3, WBS14, Calpain BM PA BTA6 BWT, W365, HCW, LMA

18. Identification of QTL in cattle What have we used to identify QTL? What have we found? Where are we validating them?

19. Germplasm Evaluation, Cycle IV (n= 6) 52 ------- PH PA Dam line Total (n= 7) ------- 96 (n= 35) 35 41 (n= 5) 52 ------- (n= 5) ------- 47 Sire line (n= 6) 117 184 25 % Piedmontese 75 % Piedmontese 50% Piedmontese 50% Piedmontese (n = 71) (n = 109)

20. Germplasm Evaluation, Cycle V Dam:Hereford MARC III Angus n = 1551 (from 1998 to 1999) F1F1F1F1 BB(F 1 ) Ch(F 1 ) (Cundiff et al., 1998, 1999, 2000)

21. Germplasm Evaluation, Cycle V n = 154 (from 1998 to 1999) F 2 subpopulation (Cundiff et al., 1998, 1999, 2000)

22. Germplasm Evaluation, Cycle VI Dam:Hereford MARC III Angus n = 820 (from 2001 to 2002) F1F1F1F1 Ch(F 1 ) (Cundiff et al., 1998, 1999, 2000) (N= 415) Sire:HerefordAngusWagyu Norwegian Red Swedish Red & White Friesian

23. Germplasm Evaluation, Cycle VII Sire:Hereford,Angus, Red Angus, Limousin,Charolais,Simmental,Gelbvieh Dam:Hereford MARC III Angus n = 1400 (from 1999 to 2001) F1F1F1F1 (Cundiff et al., 1998, 1999, 2000) F2F2F2F2 Approximately 600/year (from 2003 and on)

24. Germplasm Evaluation, Cycle VIII Dam:Hereford MARC III Angus n = 1200 n = 1200 (from 2001 to 2002) F1F1F1F1 (Cundiff et al., 1998, 1999, 2000) Terminal cross (Approximately 600/year) Sire:HerefordAngusBeefmasterBrangusBonsmaraRomosinuano

25. STARS Brahman cattle project (Riley et al., 2002) 504 offspring samples obtained from 1995 to 1999

26. Calving Ease Selection (CE) HeiferCalvingDifficulty BirthWeight EBV, lb

27. Characterization of the variation of Myostatin (BTA2) in resource populations. GPE IV GPE V BM PA

28. Characterization of variation for QTL on BTA5 for carcass traits in resource populations. BH GPE VII PA FAT, WBS14, and YG REA, Marbling, FATYD

29. BM GPE VII Characterization of variation for QTL on BTA6 for growth and carcass traits in resource populations. BWT, WWT, LWT, ADG, HCW, and REA

30. BM GPE VII Characterization of variation for QTL on BTA27 for marbling in resource populations. MARBLING

31. Characterization of variation for QTL on BTA29 for meat tenderness in resource populations. BH GPE VII PA STARS Tenderness

32. Characterization of QTL variation in resource populations. Blackie Bonzo GPE IV GPE V GPE VII BM PA GPE VI GPE VIII Calving Ease STARS