View Full Table | Close Full ViewTable 1.

Descriptive statistics in feedlot beef cattle for performance and feed efficiency in the training and validation datasets

 
Mean
SD
Minimum
Maximum
Trait1 Training Validation Training Validation Training Validation Training Validation
ADG, kg d–1 1.81 1.70 0.38 0.39 0.60 0.71 3.29 3.30
MMWT, kg 103.30 92.39 14.94 11.70 68.32 53.25 157.70 128.10
DMI, kg d–1 9.89 9.81 1.60 1.76 5.38 4.18 15.64 15.54
RFI, kg d–1 –0.12 –0.07 0.89 1.13 –5.62 –3.70 3.84 3.35
FCR, kg gain kg–1 DM 5.68 6.09 1.52 1.87 2.68 3.11 18.74 16.76
1MMWT = midpoint metabolic weight; RFI = residual feed intake; FCR = feed conversion ratio.



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Gene name, chromosome number (Bos taurus autosome (BTA), GenBank Entrez Gene Identifier, SNP name, SNP position, nucleotide change, and functional consequences for SNP discovered in silico

 
Gene BTA: gene ID SNP name SNP position1 AA change2 SNP
AMY2B 3:539383 AMY2B1 39936868 Ser/Asn G/A
AMY2B2 39935769 Arg/Arg C/T
AMY2B4 39891301 Thr/Ala A/G
LOC780933 4:780933 CT1 106362449 Ala/Ala C/T
CT2 106361029 Pro/Pro C/T
CT3 106360880 Ser/Cys C/G
CT4 106359896 Ser/Phe C/T
CT5 106359889 Ser/Ser T/C
CT6 106359796 Ala/Ala C/T
PRSS2 4: 282603 TRYP81 106888934 Ala/Ala A/G
PTI 13:404172 PTI2 74947682 Val/Ile C/T
PTI3 74947651 Ala/Val G/A
PTI4 74944796 Pro/Ser C/T
PTI6 74944705 Arg/Lys G/A
UCP2 15:281562 UCP22 54197781 Ala/Ala T/C
UCP23 54197685 Ala/Ala A/G
UCP24 54197451 Tyr/Tyr C/T
1The SNP position is based on Bos taurus UMD 3.1, Genome Build 37.3 (Zimin et al., 2009).
2The effect of mutation (SNP) on the AA sequence.



View Full Table | Close Full ViewTable 3.

Gene name, GenBank Entrez Gene Identifier, chromosome number, SNP name, SNP position, nucleotide change, and functional consequences for SNP reported in the National Center for Biotechnology Information

 
Gene BTA and gene bank ID1 SNP name Accession number SNP position2 AA change3 SNP
AMY2B 3:539383 AMY2B6 rs42312301 39931232 Asp/Asn G/A
PRSS2 4: 282603 TRYP82 rs41256900 106888943 Ser/Ser C/T
TRYP83 rs41256901 106890553 Ser/Phe T/C
ATP6V1B2 8:338082 ATPase1 rs43563470 67810773 Asp/Asp C/T
ATPase2 rs43562811 67823611 3′ UTR C/T
ATPase3 rs43562810 67823802 3′ UTR C/T
ATPase4 rs43562809 67824091 3′ UTR A/G
PTI 13:404172 PTI1 rs43024409 74947703 Met/Leu A/T
PTI5 rs41257167 74944767 Ile/Met T/G
PTI8 rs430243454 74943702 3′ near gene T/C
CCKBR 15:281665 CCKBR1 rs42670351 47386394 Arg/Arg A/C
CCKBR2 rs42670352 47385604 Ala/Ala G/T
CCKBR3 rs42670353 47385334 Phe/Phe C/T
UCP2 15:281562 UCP21 rs41255549 54199080 Ala/Ala G/T
UCP25 rs41774217 54196971 Cys/Cys A/G
PC 29:338471 PC1 rs42194938 45602034 Intronic A/G
PC2 rs42194937 45601239 Intronic G/T
PC3 rs42195008 45529368 Ile/Ile A/G
PC4 rs42197374 45510553 Val/Ile A/G
PC5 rs42197375 45510113 Tyr/Tyr C/T
PC6 rs42197376 45508443 3′ UTR A/G
1BTA = Bos taurus autosome.
2The SNP position is from Bos taurus UMD_3.1, Genome Build 37.3 (Zimin et al., 2009).
3The effect of mutation (SNP) on AA sequence. UTR = the untranslated region.
4This SNP was merged to rs41257168 SNP.



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Genotypic and minor allele frequencies and the Hardy-Weinberg equilibrium for SNP in the discovery population

 
Gene SNP Genotype frequency MAF1 G2
AMY2B rs42312301 GG (0.000) AG (0.999) AA (0.001) 0.50 1,306.803
ATP6V1B2 rs43563470 CC (0.853) CT (0.139) TT (0.007) 0.08 0.33
rs43562811 TT (0.592) CT (0.356) CC (0.052) 0.23 0.02
rs43562810 TT (0.885) CT (0.113) CC (0.002) 0.06 0.61
rs43562809 AA (0.008) AG (0.144) GG (0.847) 0.08 0.54
CCKBR rs42670351 AA (0.598) AC (0.350) CC (0.051) 0.23 0
rs42670352 TT (0.957) GT (0.004) GG (0.039) 0.04 280.853
rs42670353 TT (0.297) CT (0.481) CC (0.221) 0.46 0.93
LOC780933 CT2 CC (0.002) CT (0.999) TT (0.002) 0.50 1,301.403
CT5 CC (0.133) CT (0.867) TT (0.001) 0.43 714.553
PC rs42194938 AA (0.522) AG (0.405) GG (0.073) 0.28 0.24
rs42194937 GG (0.944) GT (0.055) TT (0.001) 0.03 0.06
rs42195008 GG (0.942) AG (0.057) AA (0.001) 0.03 0.04
rs42197374 GG (0.571) GA (0.000) AA (0.429) 0.43 9.563
rs42197375 TT (0.733) CT (0.248) CC (0.019) 0.14 0.14
rs42197376 GG (0.943) AG (0.056) AA (0.001) 0.03 0.04
PTI rs43024409 AA (0.000) AT (0.531) TT (0.469) 0.27 188.043
PTI2 CC (0.187) CT (0.812) TT (0.001) 0.41 571.123
PTI3 GG (0.747) AG (0.253) AA (0.000) 0.13 34.863
rs41257167 GG (0.007) GT (0.993) TT (0.000) 0.50 1,246.633
PRSS2 TRYP81 GG (0.451) AG (0.462) AA (0.087) 0.32 4.033
rs41256901 CC (0.679) CT (0.321) TT (0.000) 0.16 58.413
UCP2 rs41255549 TT (0.497) GT (0.413) GG (0.089) 0.30 0.07
UCP22 TT (0.603) CT (0.352) CC (0.045) 0.22 0.48
UCP23 AA (0.600) AG (0.356) GG (0.044) 0.22 1.01
UCP24 CC (0.902) CT (0.097) TT (0.001) 0.05 1.06
rs41774217 GG (0.971) AG (0.029) AA (0.000) 0.01 0.41
1MAF = minor allele frequency.
2G = the G-test statistic.
3Not in agreement with the Hardy-Weinberg equilibrium



View Full Table | Close Full ViewTable 5.

Genotypic and minor allele frequencies (MAF) for SNP in the validation population

 
Gene ID1 SNP name Accession number Genotype frequency
MAF
539383 AMY2B6 rs42312301 AA (0.000) AG (0.004) GG (0.996) 0.002
338082 ATPase1 rs43563470 TT (0.004) TC (0.133) CC (0.863) 0.07
338082 ATPase2 rs43562811 TT (0.554) TC (0.382) CC (0.063) 0.255
338082 ATPase4 rs43562809 AA (0.006) AG (0.137) GG (0.858) 0.074
281665 CCKBR1 rs42670351 AA (0.624) AC (0.319) CC (0.056) 0.216
281665 CCKRB2 rs42670352 TT (0.629) TG (0.317) GG (0.055) 0.213
281665 CCKBR3 rs42670353 TT (0.329) TC (0.496) CC (0.176) 0.423
780933 CT2 in silico TT (0.999) TC (0.000) CC (0.001) 0.001
338471 PC1 rs42194938 AA (0.062) AG (0.347) GG (0.591) 0.235
338471 PC3 rs42195008 AA (0.002) AG (0.04) GG (0.958) 0.022
338471 PC4 rs42197374 AA (0.447) AG (0.435) GG (0.119) 0.336
338471 PC5 rs42197375 TT (0.775) TC (0.211) CC (0.014) 0.119
338471 PC6 rs42197376 AA (0.003) AG (0.038) GG (0.959) 0.022
404172 PTI1 rs43024409 TT (0.131) AT (0.457) AA (0.412) 0.36
282603 TRYP81 in silico AA (0.101) AG (0.437) GG (0.462) 0.32
282603 TRYP83 rs41256901 TT (0.000) TC (0.316) CC (0.684) 0.158
281562 UCP25 rs41774217 AA (0.001) AG (0.013) GG (0.986) 0.007
1Gene ID = Entrez Gene Identifier.



View Full Table | Close Full ViewTable 6.

The extent of linkage disequilibrium (r2) between pairs of SNP within the same chromosome (Chr) in the discovery population

 
BTA1 SNP12 SNP22 r2 BTA SNP1 SNP2 r2
15 rs42670353 rs42670352 0.048 8 rs43563470 rs43562811 0.294
15 rs42670353 rs42670351 0.307 8 rs43563470 rs43562810 0.662
15 rs42670353 rs41774217 0.009 8 rs43563470 rs43562809 0.965
15 rs42670353 UCP24 0.006 8 rs43562811 rs43562810 0.215
15 rs42670353 UCP23 0.065 8 rs43562811 rs43562809 0.304
15 rs42670353 UCP22 0.064 8 rs43562810 rs43562809 0.706
15 rs42670353 rs41255549 0.014 13 rs41257167 PTI3 0.129
15 rs42670352 rs42670351 0.145 13 rs41257167 PTI2 0.116
15 rs42670352 rs41774217 0.004 13 rs41257167 rs43024409 0.157
15 rs42670352 UCP24 0.002 13 PTI3 PTI2 0.191
15 rs42670352 UCP23 0 13 PTI3 rs43024409 0.004
15 rs42670352 UCP22 0 13 PTI2 rs43024409 0.087
15 rs42670352 rs41255549 0.003 4 CT2 CT5 0.761
15 rs42670351 rs41774217 0.034 4 CT2 TRYP81 0.243
15 rs42670351 UCP24 0 4 CT2 rs41256901 0
15 rs42670351 UCP23 0.032 4 CT5 TRYP81 0.185
15 rs42670351 UCP22 0.032 4 CT5 rs41256901 0
15 rs42670351 rs41255549 0.094 4 TRYP81 rs41256901 0.055
15 rs41774217 UCP24 0.001 29 rs42197376 rs42197375 0.186
15 rs41774217 UCP23 0.004 29 rs42197376 rs42195008 0.982
15 rs41774217 UCP22 0.004 29 rs42197376 rs42194937 0.964
15 rs41774217 rs41255549 0.002 29 rs42197376 rs42194938 0.077
15 UCP24 UCP23 0.182 29 rs42197375 rs42195008 0.182
15 UCP24 UCP22 0.183 29 rs42197375 rs42194937 0.179
15 UCP24 rs41255549 0.021 29 rs42197375 rs42194938 0.003
15 UCP23 UCP22 0.991 29 rs42195008 rs42194937 0.982
15 UCP23 rs41255549 0.115 29 rs42195008 rs42194938 0.079
15 UCP22 rs41255549 0.117 29 rs42194937 rs42194938 0.078
1BTA = Bos taurus autosome.
2SNP1 = single nucleotide polymorphism in locus 1; SNP2 = single nucleotide polymorphism in locus 2.



View Full Table | Close Full ViewTable 7.

Estimates of allele substitution effects and genotypic effects (least squares means) of SNP in gene protease serine 2 (trypsin 2; PRSS2) in the discovery population

 
Genotype as fixed effect
Allele substitution effect
LSM3 ± SE LSM ± SE LSM ± SE
Trait1 SNP name P-value RA2 Estimate ± SE P-value C/C (G/G) C/T (A/G) T/T (A/A)
ADG rs41256901 0.128 T 0.038 ± 0.02 0.128 1.659 ± 0.048 1.697 ± 0.048
TRYP81 0.595 A 0.01 ± 0.02 0.737 1.668 ± 0.048 1.668 ± 0.048 1.698 ± 0.048
DMI rs41256901 0.084 T –0.184 ± 0.11 0.084 9.596 ± 0.20 9.412 ± 0.20
TRYP81 0.189 A 0.101 ± 0.08 0.295 9.464 ± 0.20 9.621 ± 0.20 9.597 ± 0.20
FCR rs41256901 <0.001** T –0.293 ± 0.08 <0.001** 6.201 ± 0.16 5.909 ± 0.16
TRYP81 0.332 A 0.059 ± 0.06 0.421 6.104 ± 0.149 6.21 ± 0.149 6.163 ± 0.149
MMWT rs41256901 0.627 T –0.331 ± 0.69 0.627 102.4 ± 1.331 102.069 ± 1.33
TRYP81 0.279 A 0.549 ± 0.5 0.058 101.599 ± 1.25 103.071 ± 1.25 101.536 ± 1.25
RFI rs41256901 0.010* T –0.199 ± 0.08 0.010* –0.141 ± 0.146 –0.34 ± 0.146
TRYP81 0.478 A 0.039 ± 0.06 0.766 –0.216 ± 0.147 –0.186 ± 0.147 –0.126 ± 0.147
Tended to affect the trait before the modified Bonferroni adjustment for multiple testing (P < 0.10).
Significant after the modified Bonferroni adjustment for multiple testing (P < 0.05).
*Significant effect before the modified Bonferroni adjustment for multiple testing (P < 0.05).
**Significant effect before the modified Bonferroni adjustment for multiple testing (P < 0.01).
1ADG = average daily gain (kg d–1); DMI = daily dry matter intake (kg d–1); FCR = feed conversion ratio (kg gain kg–1 DM); MMWT = midpoint metabolic weight (kg); RFI = residual feed intake (kg d–1).
2RA = substitution allele.
3LSM = least squares mean.



View Full Table | Close Full ViewTable 8.

Estimates of allele substitution effects and genotypic effects (least squares means) of SNP in gene cholecystokinin B receptor (CCKBR) in the discovery population

 
Genotype as fixed effect
Allele substitution effect
LSM3 ± SE LSM ± SE LSM ± SE
Trait1 SNP name P-value RA2 Estimate ± SE P-value C/C (G/G) C/T (A/G) T/T (A/A)
ADG rs42670353 0.006** T –0.043 ± 0.02 0.019* 1.73 ± 0.05 1.67 ± 0.05 1.64 ± 0.05
rs42670351 0.135 C 0.03 ± 0.02 0.112 1.66 ± 0.05 1.70 ± 0.05 1.65 ± 0.05
rs42670352 0.427 G –0.024 ± 0.03 0.620 1.63 ± 0.05 1.56 ± 0.05 1.67 ± 0.05
DMI rs42670352 0.055 G –0.236 ± 0.12 0.033* 9.14 ± 0.20 8.28 ± 0.20 9.52 ± 0.20
rs42670351 0.467 C –0.06 ± 0.08 0.069 9.08 ± 0.20 10.00 ± 0.20 9.53 ± 0.20
rs42670353 0.563 T –0.038 ± 0.07 0.828 9.61 ± 0.20 9.55 ± 0.20 9.53 ± 0.20
FCR rs42670353 0.033* T 0.114 ± 0.05 0.055 5.92 ± 0.16 6.12 ± 0.16 6.16 ± 0.16
rs42670351 0.194 C –0.087 ± 0.07 0.405 6.00 ± 0.15 6.14 ± 0.151 6.21 ± 0.15
rs42670352 0.673 G –0.041 ± 0.1 0.727 6.12 ± 0.17 5.82 ± 0.17 6.17 ± 0.17
MMWT rs42670353 0.229 T –0.523 ± 0.43 0.306 103.44 ± 1.33 102.28 ± 1.33 102.3 ± 1.33
rs42670351 0.391 C –0.467 ± 0.54 0.689 101.42 ± 1.24 102.01 ± 1.24 102.45 ± 1.24
rs42670352 0.490 G –0.55 ± 0.8 0.396 100.33 ± 1.36 105.66 ± 1.36 101.82 ± 1.36
RFI rs42670352 0.053 G –0.175 ± 0.09 0.002 –0.42 ± 0.15 –1.61 ± 0.15 –0.18 ± 0.15
rs42670353 0.280 T 0.052 ± 0.05 0.434 –0.30 ± 0.15 –0.19 ± 0.15 –0.19 ± 0.15
rs42670351 0.355 C –0.056 ± 0.06 0.028* –0.60 ± 0.15 –0.16 ± 0.15 –0.21 ± 0.15
Tended to affect the trait before the modified Bonferroni adjustment for multiple testing (P < 0.10)
Significant after the modified Bonferroni adjustment for multiple testing (P < 0.05)
*Significant effect before the modified Bonferroni adjustment for multiple testing (P < 0.05)
**Significant effect before the modified Bonferroni adjustment for multiple testing (P < 0.01)
1ADG = average daily gain (kg d–1); DMI = daily dry matter intake (kg d–1); FCR = feed conversion ratio (kg gain kg–1 DM); MMWT = midpoint metabolic weight (kg); RFI = residual feed intake (kg d–1).
2RA = substitution allele.
3LSM = least squares mean.



View Full Table | Close Full ViewTable 9.

Estimates of allele substitution effects on feed efficiency traits in the validation study

 
BTA: gene ID1 Trait2 SNP name Ref_SNP n3 MA4 MAF5 Estimate ± SE P-value6
8: 338082 MMWT ATPase4 rs43562809 726 A 0.073 1.292 ± 0.76 0.0897 d
8: 338082 FCR ATPase2 rs43562811 726 C 0.252 –0.139 ± 0.06 0.0218 d
8: 338082 ADG ATPase2 rs43562811 726 C 0.252 0.037 ± 0.02 0.0277
8: 338082 MMWT ATPase2 rs43562811 726 C 0.252 0.941 ± 0.45 0.0378
13: 404172 MMWT PTI1 rs43024409 698 T 0.352 0.973 ± 0.43 0.0234
13: 404172 ADG PTI1 rs43024409 698 T 0.352 0.026 ± 0.02 0.0970
15: 281665 DMI CCRB3 rs42670353 725 G 0.420 –0.251 ± 0.07 0.0008 d
15: 281665 RFI CCRB3 rs42670353 725 G 0.420 –0.159 ± 0.06 0.0135
15: 281665 FCR CCRB3 rs42670353 725 G 0.420 –0.125 ± 0.05 0.0168 sd*
15: 281665 DMI CCRB2 rs42670352 725 G 0.217 –0.222 ± 0.09 0.0116 sd*
15: 281665 RFI CCRB2 rs42670352 725 G 0.217 –0.139 ± 0.08 0.0658 sd*
15: 281665 FCR CCRB2 rs42670352 725 G 0.217 –0.099 ± 0.06 0.106 d
15: 281665 DMI CCRB1 rs42670351 700 C 0.221 –0.235 ± 0.09 0.0084 d
15: 281665 RFI CCRB1 rs42670351 700 C 0.221 –0.164 ± 0.08 0.0315 d*
15: 281665 FCR CCRB1 rs42670351 700 C 0.221 –0.117 ± 0.06 0.0589 d
Significant after the modified Bonferroni adjustment for multiple testing (P < 0.05) in the validation population.
1BTA = Bos taurus autosome; gene ID = Entrez Gene Identifier.
2ADG = average daily gain (kg d–1); DMI = daily dry matter intake (kg d–1); FCR = feed conversion ratio (kg gain kg–1 DM); MMWT = midpoint metabolic weight (kg); RFI = residual feed intake (kg d–1).
3n = the number of records used in the analyses.
4MA = minor allele.
5MAF = minor allele frequency.
6d = The same direction but was not significant in the discovery population; d = the same direction but showed a trend (P = 0.069) in the discovery population using the genotypic model; sd* = the same direction and significance was found for both the discovery and validation populations; d* = the same direction and significance was found for both the discovery and validation populations using the genotypic model.



View Full Table | Close Full ViewTable 10.

The genotypic analysis for SNP affecting feed efficiency traits in the validation population

 
LSM7 ± SE LSM ± SE LSM ± SE
BTA1 Gene ID2 SNP name Ref. SNP3 MA4 Trait5 P-value MAF6 C/C (GG) C/T (A/G) T/T (A/A)
8 338082 ATPase2 rs43562811 C ADG 0.058 0.255 1.76 ± 0.03 1.70 ± 0.03 1.67 ± 0.03
8 338082 ATPase2 rs43562811 C FCR 0.067 0.255 6.59 ± 0.12 6.75 ± 0.12 6.89 ± 0.12
8 338082 ATPase2 rs43562811 C MMWT 0.037 0.255 106.33 ± 0.87 104.09 ± 0.87 103.53 ± 0.87
13 404172 PTI1 rs43024409 T MMWT 0.082 0.36 105.03 ± 0.88 104.41 ± 0.88 103.31 ± 0.88
15 281665 CCKBR1 rs42670351 C DMI 0.009 0.216 10.22 ± 0.16 10.69 ± 0.16 10.87 ± 0.16
15 281665 CCKBR1 rs42670351 C FCR 0.085 0.216 6.58 ± 0.12 6.66 ± 0.12 6.82 ± 0.12
15 281665 CCKBR1 rs42670351 C RFI 0.014 0.216 –0.18 ± 0.13 0.04 ± 0.13 0.25 ± 0.13
15 281665 CCKBR2 rs42670352 G DMI 0.011 0.213 10.22 ± 0.16 10.689 ± 0.16 10.85 ± 0.16
15 281665 CCKBR2 rs42670352 G FCR 0.107 0.213 6.63 ± 0.12 6.72 ± 0.12 6.86 ± 0.12
15 281665 CCKBR2 rs42670352 G RFI 0.024 0.213 –0.16 ± 0.13 0.085 ± 0.13 0.26 ± 0.13
15 281665 CCKBR3 rs42670353 G DMI 0.002 0.423 10.48 ± 0.16 10.70 ± 0.16 10.98 ± 0.16
15 281665 CCKBR3 rs42670353 G FCR 0.048 0.423 6.68 ± 0.1178 6.80 ± 0.1178 6.94 ± 0.1178
15 281665 CCKBR3 rs42670353 G RFI 0.005 0.423 0.0003 ± 0.13 0.13 ± 0.13 0.38 ± 0.13
29 338471 PC5 rs42197375 C MMWT 0.062 0.119 108.98 ± 0.87 103.986 ± 0.87 104.56 ± 0.87
1BTA = Bos taurus autosome.
2Gene ID = Entrez Gene Identifier.
3Ref. SNP = SNP reference number at the National Center for Biotechnology Information.
4MA = minor allele.
5ADG = average daily gain (kg d–1); DMI = daily dry matter intake (kg d–1); FCR = feed conversion ratio (kg gain kg–1 DM); MMWT = midpoint metabolic weight (kg); RFI = residual feed intake (kg d–1)
6MAF = minor allele frequency.
7LSM = least squares mean.



View Full Table | Close Full ViewAppendix 1.

Biological mechanisms, molecular function, and pathways associated with the candidate genes in the study

 
Category1 Gene ontology term P-value2 Genes
BP GO:0007586∼digestion 0.013025 282603, 780933
PATH bta04080:Neuroactive ligand-receptor interaction 0.021155 282603, 780933, 281665
MF GO:0004252∼serine-type endopeptidase activity 0.062294 282603, 780933
MF GO:0008236∼serine-type peptidase activity 0.070418 282603, 780933
MF GO:0017171∼serine hydrolase activity 0.070923 282603, 780933
MF GO:0004175∼endopeptidase activity 0.156439 282603, 780933
MF GO:0070011∼peptidase activity, acting on L-amino acid peptides 0.201141 282603, 780933
BP GO:0055085∼transmembrane transport 0.202684 281562, 338082
MF GO:0008233∼peptidase activity 0.207363 282603, 780933
MF GO:0016787∼hydrolase activity 0.212711 282603, 780933, 338082
MF GO:0005509∼calcium ion binding 0.252329 282603, 780933
BP GO:0006508∼proteolysis 0.304393 282603, 780933
MF GO:0003824∼catalytic activity 0.343324 282603, 780933, 338082, 338471
MF GO:0046872∼metal ion binding 0.378607 282603, 780933, 338471
MF GO:0043169∼cation binding 0.384751 282603, 780933, 338471
MF GO:0043167∼ion binding 0.390012 282603, 780933, 338471
MF GO:0005515∼protein binding 0.704959 282603, 780933, 281665
MF GO:0005488∼binding 0.773127 282603, 780933, 281562, 281665, 338471
MF GO:0004857∼enzyme inhibitor activity 1 404172
MF GO:0004866∼endopeptidase inhibitor activity 1 404172
MF GO:0004867∼serine-type endopeptidase inhibitor activity 1 404172
BP GO:0005996∼monosaccharide metabolic process 1 338471
BP GO:0006006∼glucose metabolic process 1 338471
BP GO:0006091∼generation of precursor metabolites and energy 1 338082
BP GO:0006094∼gluconeogenesis 1 338471
BP GO:0006119∼oxidative phosphorylation 1 338082
BP GO:0006163∼purine nucleotide metabolic process 1 338082
BP GO:0006754∼ATP biosynthetic process 1 338082
BP GO:0006793∼phosphorus metabolic process 1 338082
BP GO:0006811∼ion transport 1 338082
BP GO:0006812∼cation transport 1 338082
BP GO:0006818∼hydrogen transport 1 338082
BP GO:0006839∼mitochondrial transport 1 281562
BP GO:0006874∼cellular calcium ion homeostasis 1 281665
BP GO:0007166∼cell surface receptor linked signal transduction 1 281665
BP GO:0007186∼G-protein coupled receptor protein signaling pathway 1 281665
BP GO:0008284∼positive regulation of cell proliferation 1 281665
BP GO:0008610∼lipid biosynthetic process 1 338471
BP GO:0009057∼macromolecule catabolic process 1 282603
BP GO:0009141∼nucleoside triphosphate metabolic process 1 338082
BP GO:0009205∼purine ribonucleoside triphosphate metabolic process 1 338082
BP GO:0015985∼energy coupled proton transport, down electrochemical gradient 1 338082
BP GO:0015986∼ATP synthesis coupled proton transport 1 338082
BP GO:0015992∼proton transport 1 338082
BP GO:0016051∼carbohydrate biosynthetic process 1 338471
BP GO:0016310∼phosphorylation 1 338082
BP GO:0019318∼hexose metabolic process 1 338471
BP GO:0030003∼cellular cation homeostasis 1 281665
BP GO:0030163∼protein catabolic process 1 282603
MF GO:0030234∼enzyme regulator activity 1 404172
BP GO:0032963∼collagen metabolic process 1 282603
BP GO:0034220∼ion transmembrane transport 1 338082
BP GO:0034404∼nucleobase, nucleoside and nucleotide biosynthetic process 1 338082
BP GO:0034637∼cellular carbohydrate biosynthetic process 1 338471
BP GO:0034654∼nucleobase, nucleoside, nucleotide and nucleic acid biosynthetic process 1 338082
BP GO:0042127∼regulation of cell proliferation 1 281665
BP GO:0044257∼cellular protein catabolic process 1 282603
BP GO:0044259∼multicellular organismal macromolecule metabolic process 1 282603
BP GO:0044271∼nitrogen compound biosynthetic process 1 338082
BP GO:0046034∼ATP metabolic process 1 338082
BP GO:0046364∼monosaccharide biosynthetic process 1 338471
BP GO:0046907∼intracellular transport 1 281562
BP GO:0050801∼ion homeostasis 1 281665
BP GO:0051480∼cytosolic calcium ion homeostasis 1 281665
BP GO:0051603∼proteolysis involved in cellular protein catabolic process 1 282603
BP GO:0055065∼metal ion homeostasis 1 281665
BP GO:0055074∼calcium ion homeostasis 1 281665
PATH bta00620:Pyruvate metabolism 1 338471
PATH bta00500:Starch and sucrose metabolism 1 539383
PATH bta00190:Oxidative phosphorylation 1 338082
PATH bta00020:Citrate cycle (TCA cycle) 1 338471
PATH bta04020:Calcium signaling pathway 1 281665
1BP = biological process; PATH = KEGG biological pathway; MF = molecular function.
2P-value = the P-value produced by enrichment analysis using DAVID software (Huang et al., 2009).



View Full Table | Close Full ViewAppendix 2.

Reported QTL in the Animal QTL database overlapping with candidate genes

 
Gene name QTL name1 QTL start position (bp) QTL end position Trait
AMY2B QTL_10129 34002036 65739450 Milk fat yield (daughter deviation)
AMY2B QTL_10683 29956341 43937012 Height (mature)
AMY2B QTL_10684 23481347 43937012 BW (birth)
AMY2B QTL_10685 23481347 43937012 BW (weaning)
AMY2B QTL_10686 29956341 43937012 Height (yearling)
AMY2B QTL_10687 23481347 43937012 Carcass weight
AMY2B QTL_1326 17737279 42568866 BW (birth)
AMY2B QTL_1351 37151994 48988111 Marbling score
AMY2B QTL_2437 17033086 46894623 Milk protein yield
AMY2B QTL_2442 20288493 43373658 Milk fat percentage
AMY2B QTL_2443 18441472 63526272 Milk protein percentage
AMY2B QTL_2490 0 43937012 Somatic Cell Count
AMY2B QTL_2541 28000529 90939023 Marbling score
AMY2B QTL_2584 22194674 57994437 Milk yield
AMY2B QTL_2653 29300268 47891582 Milk yield
AMY2B QTL_2654 29300268 47891582 Milk protein percentage
AMY2B QTL_2657 29300268 48706434 Milk protein yield
ATP6V1B2 QTL_10831 62732685 70703039 Calving ease (direLOC780933)
ATP6V1B2 QTL_10832 62732685 83158666 BW (birth)
ATP6V1B2 QTL_11442 46113400 92708598 Dystocia (maternal)
ATP6V1B2 QTL_11443 46113400 92708598 Stillbirth (maternal)
ATP6V1B2 QTL_1683 62735433 83360187 Somatic Cell Count
ATP6V1B2 QTL_1684 62735433 83360187 StruLOC780933ural soundness (legs
ATP6V1B2 QTL_2497 43089984 83569900 Clinical mastitis
ATP6V1B2 QTL_2498 43089984 83569900 Somatic Cell Count
ATP6V1B2 QTL_3599 59682392 103895369 Foot angle
CCKBR QTL_10993 32063789 47949409 Height (mature)
CCKBR QTL_10994 32063789 47949409 Carcass weight
CCKBR QTL_10995 32063789 47949409 Longissimus muscle area
CCKBR QTL_12195 32881427 55518119 Liver percentage
CCKBR QTL_1335 21718187 54967641 Kidney
CCKBR QTL_1596 40000451 47942043 Udder attachment
CCKBR QTL_1598 40000451 47942043 Stature
CCKBR QTL_1601 40000451 47942043 Udder depth
CCKBR QTL_1699 15363886 47946463 Rump angle
CCKBR QTL_2678 40000451 47942043 Somatic cell score
LOC780933 QTL_10515 98051474 119280357 Parasites mean of natural logarithm
LOC780933 QTL_10716 95179745 107915671 BW (mature)
LOC780933 QTL_10717 81300315 107915671 Fat thickness at the 12th rib
LOC780933 QTL_10718 95179745 113949759 Scrotal circumference
LOC780933 QTL_4485 98051474 107905229 Postweaning average daily gain
LOC780933 QTL_5055 57599923 119280357 Milk fat percentage
PC QTL_11297 37089419 48660164 Carcass weight
PC QTL_11298 37089419 48660164 BW (yearling)
PC QTL_11299 37089419 51080436 BW (birth)
PC QTL_11301 37089419 48660164 BW (weaning)
PC QTL_1343 34055421 46031383 Retail produLOC780933 yield
PC QTL_1345 27433819 48199160 Tenderness score
PC QTL_1373 36423729 46550490 Tenderness score
PC QTL_1374 37521610 51800755 Tenderness score
PC QTL_1380 32188341 45594750 BW at castration
PC QTL_1664 35467866 46211463 Foot angle
PC QTL_1665 35467866 46211463 StruLOC780933ural soundness (legs
PC QTL_1717 26859725 48660164 Teat placement
PC QTL_1722 26859725 48660164 Twinning
PC QTL_2593 18168758 46211940 Milk yield
PC QTL_2612 18168758 46211940 Milk protein yield
PC QTL_4506 37089419 48660164 305 d milk yield
PC QTL_4651 35465705 46211940 Rump angle
PC QTL_4851 34170672 51606269 Juiciness
PC QTL_4852 34170672 51606269 Shear force
PC QTL_4853 34170672 51606269 Tenderness score
PC QTL_5371 1983481 45887319 Gestation length
PC QTL_7153 34170672 51606269 Flight from feeder
PC QTL_7154 34170672 51606269 Flight fm feeder
PC QTL_7154 34170672 51606269 Flight from feeder
PTI QTL_10946 50098085 77464923 Weaning weight-maternal milk
PTI QTL_10947 60604089 77464923 Marbling score (EBV)
PTI QTL_10948 60604089 77464923 Longissimus muscle area
PTI QTL_10949 71832245 77464923 BW (weaning)
PTI QTL_11446 69174400 81815003 Stillbirth (direLOC780933)
PTI QTL_1386 15506564 84433115 Teat length
PTI QTL_1584 59740226 79842537 Udder attachment
PTI QTL_1585 59740226 79842537 PTA type
PTI QTL_1586 59740226 79842537 Udder height
PTI QTL_1587 59740226 79842537 Udder width
PTI QTL_1588 59740226 79842537 Udder depth
PTI QTL_1589 59740226 79842537 Udder composite index
PTI QTL_2670 59740226 79842537 Milk yield
PTI QTL_2671 59740226 79842537 Milk protein yield
PTI QTL_2775 69333703 77472469 Somatic cell score
PTI QTL_3569 0 77464923 Heat intensity
PTI QTL_5011 71832245 77464923 Interval to first estrus after calving
PRSS2 QTL_10515 98051474 119280357 Parasites mean of natural logarithm
PRSS2 QTL_10716 95179745 107915671 BW (mature)
PRSS2 QTL_10717 81300315 107915671 Fat thickness at the 12th rib
PRSS2 QTL_10718 95179745 113949759 Scrotal circumference
PRSS2 QTL_4485 98051474 107905229 Postweaning average daily gain
PRSS2 QTL_5055 57599923 119280357 Milk fat percentage
PRSS2 QTL_10515 98051474 119280357 Parasites mean of natural logarithm
PRSS2 QTL_10716 95179745 107915671 BW (mature)
PRSS2 QTL_10717 81300315 107915671 Fat thickness at the 12th rib
PRSS2 QTL_10718 95179745 113949759 Scrotal circumference
PRSS2 QTL_4485 98051474 107905229 Postweaning average daily gain
PRSS2 QTL_5055 57599923 119280357 Milk fat percentage
UCP2 QTL_10996 47949409 60494505 Weaning weight-maternal milk
UCP2 QTL_10997 51606842 60494505 BW (mature)
UCP2 QTL_10998 47949409 60494505 BW (weaning)
UCP2 QTL_10999 51606842 60641830 Marbling score (EBV)
UCP2 QTL_11001 51606842 79392371 Height (mature)
UCP2 QTL_12195 32881427 55518119 Liver percentage
UCP2 QTL_1335 21718187 54967641 Kidney
UCP2 QTL_1594 47946463 57050270 Body form composite index
UCP2 QTL_1595 47946463 57050270 Teat placement
UCP2 QTL_1597 47946463 57050270 PTA type
UCP2 QTL_1599 47946463 57050270 Thurl width
UCP2 QTL_1600 47946463 57050270 Udder cleft
UCP2 QTL_1602 47946463 57050270 Udder composite index
UCP2 QTL_5122 50892329 55864326 Abomasum displacement
1QTL = Quantitative trait loci.