Detection of QTL in beef cattle Eduardo Casas U.S. Meat Animal Research Center, Clay Center,...
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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
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Cell
Chromosome Nucleosome
Double helixSequence
DNA structure
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Microsatellites and Single Nucleotide Polymorphisms
Alelle A
Alelle B
CCGTATCACACAGTCAAC
CCGTATCACACACACAGTCAAC
GAACTAGCTTGAC
GAACTGGCTTGAC
Microsatellites SNP
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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
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(Kappes et al., 1997)
Bovine Chromosome 2 (BTA2).
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BOVINE CHROMOSOME 5
0
2
4
6
8
10
12
14
16
Sugg.FATRPYDYGRIBFAT
Quantitative trait loci (QTL) on bovine chromosome 5
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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?
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Family from sire 921467 (BM)Family from sire 921467 (BM)
XX
XX
n= 245n= 245BMBM
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Family from sire 921690 (PA)Family from sire 921690 (PA)
XX
XX
n= 209n= 209
PAPA
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XX
XX
n= 500n= 500
Family from 906802 (Bonzo)Family from 906802 (Bonzo)
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XX
XX
n= 500n= 500
Family from 906801 (Blackie)Family from 906801 (Blackie)
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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
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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 (%).
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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?
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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
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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?
![Page 19: Detection of QTL in beef cattle Eduardo Casas U.S. Meat Animal Research Center, Clay Center, Nebraska.](https://reader038.fdocuments.us/reader038/viewer/2022110321/56649d005503460f949d209a/html5/thumbnails/19.jpg)
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)
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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)
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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)
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Germplasm Evaluation, Cycle VIGermplasm Evaluation, Cycle VI
Dam:Dam:
HerefordHerefordMARC IIIMARC IIIAngusAngus
n = 820 (from 2001 to 2002)n = 820 (from 2001 to 2002)
FF11
Ch(FCh(F11))
(Cundiff et al., 1998, 1999, 2000)(Cundiff et al., 1998, 1999, 2000)
(N= 415)(N= 415)
Sire:Sire:
HerefordHerefordAngusAngusWagyuWagyuNorwegian RedNorwegian RedSwedish Red & Swedish Red & WhiteWhiteFriesianFriesian
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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:
HerefordHerefordMARC IIIMARC IIIAngusAngus
n = 1400 n = 1400 (from 1999 to 2001)(from 1999 to 2001)
FF11
(Cundiff et al., 1998, 1999, 2000)(Cundiff et al., 1998, 1999, 2000)
FF22Approximately 600/yearApproximately 600/year(from 2003 and on)(from 2003 and on)
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Germplasm Evaluation, Cycle VIII
Dam:Dam:
HerefordHerefordMARC IIIMARC IIIAngusAngus
n = 1200 n = 1200 (from 2001 to 2002)(from 2001 to 2002)
FF11
(Cundiff et al., 1998, 1999, 2000)(Cundiff et al., 1998, 1999, 2000)
Terminal crossTerminal cross(Approximately 600/year)(Approximately 600/year)
Sire:Sire:
HerefordHerefordAngusAngusBeefmasterBeefmasterBrangusBrangusBonsmaraBonsmaraRomosinuanoRomosinuano
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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
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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
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Characterization of the variation of Myostatin (BTA2) in resource populations.
GPE IV
GPE V
BM
PA
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Characterization of variation for QTL on BTA5 for carcass traits in resource populations.
BH
GPE VII
PAFAT, WBS14, and YG
REA, Marbling, FATYD
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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
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BM
GPE VII
Characterization of variation for QTL on BTA27 for marbling in resource populations.
MARBLING
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Characterization of variation for QTL on BTA29 for meat tenderness in resource populations.
BH
GPE VII
PA
STARS
Tenderness
Tende
rnes
s
Tenderness
Tenderness
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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