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

Detection of QTL in beef cattleDetection of QTL in beef cattle

Eduardo CasasEduardo Casas

U.S. Meat Animal Research Center,U.S. Meat Animal Research Center,Clay Center, NebraskaClay Center, Nebraska

Cell

Chromosome Nucleosome

Double helixSequence

DNA structure

Microsatellites and Single Nucleotide Polymorphisms

Alelle A

Alelle B

CCGTATCACACAGTCAAC

CCGTATCACACACACAGTCAAC

GAACTAGCTTGAC

GAACTGGCTTGAC

Microsatellites SNP

Da

m

11 22 33 44 55 88 1010 1111

Microsatellites

Sire allele 1

Sire allele 2

Dam allele 1

Dam allele 2

Sir

e

(Kappes et al., 1997)

Bovine Chromosome 2 (BTA2).

BOVINE CHROMOSOME 5

0

2

4

6

8

10

12

14

16

Sugg.FATRPYDYGRIBFAT

Quantitative trait loci (QTL) on bovine chromosome 5

Identification of QTL in cattleIdentification of QTL in cattle

What have we used to identify QTL?What have we used to identify QTL?

What have we found?What have we found?

Where are we validating them?Where are we validating them?

Family from sire 921467 (BM)Family from sire 921467 (BM)

XX

XX

n= 245n= 245BMBM

Family from sire 921690 (PA)Family from sire 921690 (PA)

XX

XX

n= 209n= 209

PAPA

XX

XX

n= 500n= 500

Family from 906802 (Bonzo)Family from 906802 (Bonzo)

XX

XX

n= 500n= 500

Family from 906801 (Blackie)Family from 906801 (Blackie)

http://www.ansi.okstate.edu/breeds/index.htmhttp://www.ansi.okstate.edu/breeds/index.htm

¼ Hereford¼ Hereford ¼ Angus¼ Angus

¼ Pinzgauer¼ Pinzgauer ¼ Red Poll¼ Red Poll

MARC IIIMARC III

Traits measuredTraits measured

Growth traits:Growth traits:

- Birth weight (kg).- Birth weight (kg).- Weaning weight (kg).- Weaning weight (kg).- Yearling weight (kg).- Yearling weight (kg).- Postweaning average- Postweaning average daily gain (kg/d).daily gain (kg/d).

Measured carcass traits:Measured carcass traits:

- Hot carcass weight (kg).- Hot carcass weight (kg).- Fat depth (cm).- Fat depth (cm).- Marbling score.- Marbling score.- Longissimus muscle area (cm- Longissimus muscle area (cm22).).- USDA yield grade.- USDA yield grade.-Est. kidney, pelvic, & heart fat (%).Est. kidney, pelvic, & heart fat (%).-Rib bone.Rib bone.-Ribfat.Ribfat.- Ribmus.- Ribmus.- Warner-Bratzler shear force- Warner-Bratzler shear force

2 or 3 d postmortem (kg).2 or 3 d postmortem (kg).- Warner-Bratzler shear force- Warner-Bratzler shear force

14 d postmortem (kg).14 d postmortem (kg).

Predicted carcass traits:Predicted carcass traits:

- Retail product yield (%).- Retail product yield (%).- Fat yield (%).- Fat yield (%).- Bone yield (%).- Bone yield (%).- Dressing percent (%).- Dressing percent (%).

BlackieBlackieBonzoBonzo

GENOME SCAN RESULTS IN ALL RESOURCE FAMILIESGENOME SCAN RESULTS IN ALL RESOURCE FAMILIES

BTA2

MSTN

BTA1

RPYDFATYD MARB, RPYD

MARB

BTA3

MARB, RPYDMARB, RPYDFat yield

BTA4

RPYD, FATYDWBS14

HCW, WBS3

BTA5

FAT, YG, RPYD, WBS14RIBBONE, DP, RIBFAT, BWT

BTA8

FAT, MARBFAT

BTA15

WBS14

BTA27

MARBDairy Form

BTA29

WBS3, WBS14, Calpain

BM PA

BTA6

BWT, W365,HCW, LMA

Germplasm Evaluation, Cycle IVGermplasm Evaluation, Cycle IV

(n= 6) (n= 6) 52 -------52 -------

PHPH

PAPA

Dam lineDam line

TotalTotal

(n= 7) (n= 7) ------- 96------- 96

(n= 35) (n= 35) 35 4135 41

(n= 5) (n= 5) 52 -------52 -------

(n= 5) (n= 5) ------- 47------- 47

Sire lineSire line

(n= 6) (n= 6) 117 184117 184

25 % Piedmontese25 % Piedmontese

75 % Piedmontese75 % Piedmontese

50% Piedmontese50% Piedmontese

(n = 71)(n = 71) (n = 109)(n = 109)

Germplasm Evaluation, Cycle VGermplasm Evaluation, Cycle V

Dam:Dam:

HerefordHerefordMARC IIIMARC IIIAngusAngus

n = 1551 (from 1998 to 1999)n = 1551 (from 1998 to 1999)

FF11

BB(FBB(F11)) Ch(FCh(F11))

(Cundiff et al., 1998, 1999, 2000)(Cundiff et al., 1998, 1999, 2000)

Germplasm Evaluation, Cycle VGermplasm Evaluation, Cycle V

n = 154 (from 1998 to 1999)n = 154 (from 1998 to 1999)

FF22 subpopulation subpopulation

(Cundiff et al., 1998, 1999, 2000)

Germplasm Evaluation, Cycle VIGermplasm Evaluation, Cycle VI

Dam:Dam:


n = 820 (from 2001 to 2002)n = 820 (from 2001 to 2002)

FF11

Ch(FCh(F11))


(N= 415)(N= 415)

Sire:Sire:

HerefordHerefordAngusAngusWagyuWagyuNorwegian RedNorwegian RedSwedish Red & Swedish Red & WhiteWhiteFriesianFriesian

Germplasm Evaluation, Cycle VIIGermplasm Evaluation, Cycle VII

Sire:Sire:

Hereford, Hereford, Angus, Angus, Red Angus,Red Angus,Limousin,Limousin,Charolais,Charolais,Simmental,Simmental,GelbviehGelbvieh

Dam:Dam:


n = 1400 n = 1400 (from 1999 to 2001)(from 1999 to 2001)

FF11


FF22Approximately 600/yearApproximately 600/year(from 2003 and on)(from 2003 and on)

Germplasm Evaluation, Cycle VIII

Dam:Dam:


n = 1200 n = 1200 (from 2001 to 2002)(from 2001 to 2002)

FF11


Terminal crossTerminal cross(Approximately 600/year)(Approximately 600/year)

Sire:Sire:

HerefordHerefordAngusAngusBeefmasterBeefmasterBrangusBrangusBonsmaraBonsmaraRomosinuanoRomosinuano

STARS Brahman cattle projectSTARS Brahman cattle project

(Riley et al., 2002)(Riley et al., 2002)

504 offspring samples obtained from 1995 to 1999504 offspring samples obtained from 1995 to 1999

Calving Ease Selection (CE)Calving Ease Selection (CE)

18.7%

40.3%

10.3%

31.1%

0%

10%

20%

30%

40%

50%

1998 1999

-6

-4

-2

0

2

4

92 93 94 95 96 97 98 99

Control Select

Heifer Heifer CalvingCalvingDifficultyDifficulty

Birth Birth Weight Weight EBV, lbEBV, lb

Characterization of the variation of Myostatin (BTA2) in resource populations.

GPE IV

GPE V

BM

PA

Characterization of variation for QTL on BTA5 for carcass traits in resource populations.

BH

GPE VII

PAFAT, WBS14, and YG

REA, Marbling, FATYD

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

BM

GPE VII

Characterization of variation for QTL on BTA27 for marbling in resource populations.

MARBLING

Characterization of variation for QTL on BTA29 for meat tenderness in resource populations.

BH

GPE VII

PA

STARS

Tenderness

Tende

rnes

s

Tenderness

Tenderness

Characterization of QTL variation in resource populations.

Blackie

Bonzo

GPE IV

GPE V

GPE VII

BM

PA

GPE VI

GPE VIII

18.7%

40.3%

10.3%

31.1%

0%

10%

20%

30%

40%

50%

1998 1999

-6

-4

-2

0

2

4

92 93 94 95 96 97 98 99

Control Select

CalvingEase

STARS

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

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