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Descriptive statistics for growth traits1 of Charolais beef cattle

 
Trait n n(QC)2 Mean SD Minimum Maximum
BWT, kg 855 823 40.488 6.712 20 62
WWT, kg 840 809 227.554 39.571 103.7 377.8
AGW, kg 840 809 0.912 0.186 0.291 1.603
YWT, kg 418 409 356.693 58.137 211.2 582.2
PWG, kg 418 409 0.807 0.284 0.499 1.469
1AGW = preweaning ADG; BWT = BW at birth; PWG = postweaning ADG; WWT = BW at weaning; YWT = yearling BW.
2n(QC) = n after quality control.



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Parameters and statistics of SNP associated with growth traits of Charolais beef cattle1

 
Trait SNP ID2 BTA UMD3.1,3 bp Btau4.6,4 bp Allele MAF5 β,5 kg SE Percentage Var5 P-value
BWT rs42512403 15 68,021,790 66,969,167 G/A 0.44 −0.160 0.034 2.6 0.0000359
WWT rs43378829 4 30,834,682 31,656,994 C/A 0.46 −0.753 0.156 2.8 0.0000064
rs109462000 11 72,437,674 74,486,805 A/G 0.26 1.293 0.280 2.6 0.0000159
rs109028958 18 31,925,240 30,754,012 G/A 0.36 0.915 0.205 2.4 0.0000305
rs42339359 29 12,381,867 12,854,197 A/G 0.16 −1.695 0.389 2.3 0.0000442
YWT rs133575890 6 68,061,364 68,907,863 G/A 0.40 1.643 0.339 5.7 0.0000014
rs110545556 2 95,861,435 99,648,226 A/G 0.29 2.131 0.469 5.0 0.0000062
rs110875592 6 68,059,441 68,909,786 A/C 0.43 1.445 0.319 5.0 0.0000065
rs134262111 1 3,515,994 3,339,804 A/G 0.06 5.767 1.356 4.4 0.0000233
rs109532225 15 42,922,452 41,199,707 G/A 0.22 2.536 0.605 4.4 0.0000308
rs109419103 21 56,601,433 56,469,386 G/A 0.21 2.600 0.624 4.2 0.0000340
rs43538101 8 24,510,080 26,019,429 C/A 0.37 1.608 0.386 4.2 0.0000348
rs109300035 6 68,410,488 69,261,925 G/A 0.42 −1.411 0.341 4.1 0.0000380
rs135029160 6 68,027,231 68,871,374 A/G 0.45 1.317 0.319 4.1 0.0000414
AGW rs43378829 4 30,834,682 31,656,994 C/A 0.46 −0.003 0.000 2.6 0.0000176
rs109462000 11 72,437,674 74,486,805 A/G 0.26 0.005 0.001 2.5 0.0000261
PWG rs41566285 24 34,013,385 34,397,620 A/G 0.34 −0.008 0.001 5.2 0.0000058
rs41569509 9 9,372,653 8,968,100 A/C 0.41 −0.007 0.001 5.4 0.0000066
rs42219323 16 80,103,005 76,347,639 C/A 0.12 0.016 0.001 4.5 0.0000280
rs41585202 24 47,181,172 48,010,063 A/G 0.40 0.006 0.001 4.3 0.0000355
1AGW = preweaning ADG; BWT = BW at birth; PWG = postweaning ADG; WWT = BW at weaning; YWT = yearling BW.
2ID = identification.
3UMD version 3.1 (Zimin et al., 2009).
4Elsik et al. (2015).
5MAF = minimum allele frequency; β = allele substitution effect; Var = phenotypic variance explained by the SNP.



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Genes and previously reported QTL1 located near SNP associated with growth traits of Charolais beef cattle

 
Trait_SNP ID2_BTA_Mb Genes in ±250 kb QTL Reference
BWT_rs42512403_15_68.0 TRAF6, RAG1, RAG2, C15H11orf74- SNP CALEASE Sahana et al. (2011)
ADG Peters et al. (2012)
WWT, AGW_rs43378829_4_30.8 DNAH11- SNP CDCA7L- RAPGEF5 LMA and MARBL Mizoshita et al. (2004)
CALEASE Yokouchi et al. (2009)
YRLHT, MHT, MARBL, WWT, WWTMM, and YWT Thomasen et al. (2008) and McClure et al. (2010)
WWT, AGW_rs109462000_11_72.4 IFT172, KRTCAP3, NRBP1, PPM1G, ZNF513, SNX17, EIF2B4, GTF3C2, MPV17, UCN, TRIM54, DNAJC5G, SLC30A3, CAD, SLC5A6- SNP- TCF23, PRR30, PREB, ABHD1, CGREF1, KHK, EMILIN1, AGBL5, TMEM214, MAPRE3, DPYSL5 MARBL McClure et al. (2010)
WWT_rs109028958_18_31.9 CDH11- SNP SB Seidenspinner et al. (2009)
RFI Sherman et al. (2009)
WWT McClure et al. (2010)
WWT_rs42339359_29_12.3 DLG2- SNP- CCDC90B, ANKRD42, PCF11 CWT Kim et al. (2003)
CWT and TEND Casas et al. (2000, 2003)
RFI Nkrumah et al. (2007)
MHT, LMA, FATTH, CWT, and WWTMM McClure et al. (2010)
YWT_rs133575890_6_68.0
YWT_rs110875592_6_68.0
YWT_rs135029160_6_68.0
ATP10D- SNP CORIN- NFXL1
YWT_ rs109300035_6_68.4 CORIN, NFXL1, CNGA1, NIPAL1- SNP TXK- TEC
YWT_rs110545556_2_95.8 CPO- SNP KLF7- MIR2355
YWT_rs134262111_1_3.51 SNP- MIR2284I, MIR2284X
YWT_rs109532225_15_42.9 MRVI1, LYVE1, RNF141, ADM- SNP- SBF2 MHT, CALEASE, WWT, and WWTMM McClure et al. (2010)
YWT_rs109419103_21_56.6 GPR68- SNP- CCDC88C, SMEK1
YWT_rs43538101_8_24.5 - SNP SLC24A2- SB Kühn et al. (2003)
YRLHT, MHT, BWT, and CWT McClure et al. (2010)
PWG_rs41566285_24_34.0 RBBP8- SNP CALEASE, WWT, and YWT McClure et al. (2010)
PWG_rs41569509_9_9.3 SNP- COL9A1 MARBL Imai et al. (2007)
RFI Sherman et al. (2009)
CALEASE, MARBL, YWT, and WWT McClure et al. (2010)
PWG_rs42219323_16_80.1 MIR181A-1- SNP
PWG_rs41585202_24_47.1 PIAS2- SNP- KATNAL2, HDHD2, IER3IP1 FCR Sherman et al. (2009)
MARBL McClure et al. (2010)
1AGW = preweaning ADG; BWT = BW at birth; CALEASE = calving ease; CWT = carcass weight; FATTH = fat thickness at the 12th rib; FCR = feed conversion ratio; LMA = LM area; MARBL = marbling score; MHT = height at maturity; MWT = BW at maturity; PWG = postweaning ADG; RFI = residual feed intake; SB = stillbirth; TEND = tenderness score; WWT = BW at weaning; WWTMM = weaning weight-maternal milk; YWT = yearling BW; YRLHT = yearling height.
2ID = identification.



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Genes close to the SNP associated with growth traits of Charolais beef cattle

 
SNP_BTA Gene in ±250 kb Gene ID1 Distance,2 kb Description
rs42512403_15 TRAF6 539124 U 232.3 TNF (tumor necrosis factor) receptor-associated factor 6
RAG1 506302 U 191.4 Recombination activating gene 1
RAG2 782387 U 172.2 Recombination activating gene 2
C15H11orf74 614192 U 110.6 Chromosome 15 open reading frame, human C11orf74
rs43378829_4 DNAH11 497208 U 35.0 Dynein, axonemal, heavy chain 11
CDCA7L 514631 Cover Cell division cycle-associated 7-like
RAPGEF5 519566 D 182.3 Rap guanine nucleotide exchange factor (GEF) 5
rs109462000_11 IFT172 100848219 U 214.7 Intraflagellar transport 172
KRTCAP3 508550 U 212.9 Keratinocyte-associated protein 3
NRBP1 532919 U 200.3 Nuclear receptor-binding protein 1
PPM1G 286880 U 164.5 Protein phosphatase, Mg2+/Mn2+ dependent, 1G
ZNF513 100138621 U 160.5 Zinc finger protein 513
SNX17 529972 U 154.7 Sorting nexin 17
EIF2B4 521926 U 149.9 Eukaryotic translation initiation factor 2B, subunit 4 delta, 67 kDa
GTF3C2 782752 U 125.6 General transcription factor IIIC, polypeptide 2, beta 110 kDa
MPV17 505763 U 113.1 MpV17 mitochondrial inner membrane protein
UCN 518336 U 110.7 Urocortin
TRIM54 535320 U 89.1 Tripartite motif containing 54
DNAJC5G 616608 U 84.1 DnaJ (Hsp40) homolog, subfamily C, member 5 gamma
SLC30A3 512803 U 64.4 Solute carrier family 30 (Zinc transporter), member 3
CAD 504261 U 32.9 Carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase
SLC5A6 516021 U 12.2 Solute carrier family 5 (Sodium/multivitamin and iodide cotransporter),
TCF23 616841 D 32.6 Transcription factor 23
PRR30 782932 D 53.1 Proline-rich 30
PREB 525256 D 55.5 Prolactin regulatory element-binding
ABHD1 510774 D 59.6 Abhydrolase domain containing 1
CGREF1 507586 D 83.8 Cell growth regulator with EF-hand domain 1
KHK 614868 D 88.0 Ketohexokinase (fructokinase)
EMILIN1 540451 D 101.6 Elastin microfibril interfacer 1
AGBL5 538585 D 118.1 ATP/GTP-binding protein-like 5
TMEM214 514683 D 144.6 Transmembrane protein 214
MAPRE3 528839 D 160.4 Microtubule-associated protein, RP/EB family, member 3
DPYSL5 100126171 D 233.7 Dihydropyrimidinase-like 5
rs109028958_18 CDH11 785475 U 873.5 Cadherin 11, type 2, OB-cadherin (osteoblast)
rs42339359_29 DLG2 505383 U 57.7 Disks large homolog 2
CCDC90B 506046 D 78.3 Coiled-coil domain containing 90B
ANKRD42 522004 D 110.9 Ankyrin repeat domain 42
PCF11 510604 D 173.9 PCF11 cleavage and polyadenylation factor subunit
rs133575890_6
rs110875592_6
rs135029160_6
ATP10D 536495 U 138.1 ATPase, class V, type 10D
CORIN 527107 Cover Corin serine peptidase
NFXL1 784953 D 179.9 Nuclear transcription factor, X-box-binding-like 1
rs109300035_6 CORIN 527107 U 233.8 Corin serine peptidase
NFXL1 784953 U 110.8 Nuclear transcription factor, X-box-binding-like 1
CNGA1 281700 U 56.2 Cyclic nucleotide gated channel alpha 1
NIPAL1 539757 U 18.9 NIPA-like domain containing 1
TXK 504782 Cover TXK tyrosine kinase
TEC 504733 D 58.4 Tec protein tyrosine kinase
rs110545556_2 CPO 508767 U 160.5 Carboxypeptidase O
KLF7 537747 Cover Kruppel-like factor 7 (ubiquitous)
MIR2355 100313333 D 26.7 MicroRNA mir-2355
rs134262111_1 MIR2284I 100313114 D 64.2 MicroRNA mir-2284i
MIR2284X 100526413 D 91.7 MicroRNA mir-2284x
rs109532225_15 MRVI1 281918 U 247.8 Murine retrovirus integration site 1 homolog
LYVE1 404179 U 229.9 Lymphatic vessel endothelial hyaluronan receptor 1
RNF141 539455 U 168.8 Ring finger protein 141
ADM 280713 U 9.1 Adrenomedullin
SBF2 510498 D 48.5 SET-binding factor 2
rs109419103_21 GPR68 281799 U 10.1 G protein-coupled receptor 68
CCDC88C 515039 D 28.3 Coiled-coil domain containing 88C
SMEK1 407220 D 199.4 SMEK homolog 1, suppressor of mek1 (dictyostelium)
rs43538101_8 SLC24A2 525618 Cover Solute carrier family 24 (sodium/potassium/calcium exchanger), member 2
rs41566285_24 RBBP8 512977 U 65.1 Retinoblastoma-binding protein 8
rs41569509_9 COL9A1 282195 D 144.7 Collagen, type IX, alpha 1
rs42219323_16 MIR181A-1 100313401 U 417.0 MicroRNA mir-181a-1
rs41585202_24 PIAS2 533403 U 183.6 Protein inhibitor of activated STAT, 2
KATNAL2 514354 D 4.2 Katanin p60 subunit A-like 2
HDHD2 505403 D 64.9 Haloacid dehalogenase-like hydrolase domain containing 2
IER3IP1 768079 D 123.7 Immediate early response 3 interacting protein 1
1ID = identification.
2D = downstream; U = upstream.



View Full Table | Close Full ViewTable 5.

Previously reported QTL1 found near the SNP associated with growth traits of Charolais beef cattle

 
Trait_SNP ID2_BTA_Mb QTL QTL ID QTL in Btau4.6,3 bp QTL reference
BWT_rs42512403_15_68.0 ADG 22798 66,162,109–75,437,676 Peters et al. (2012)
CALEASE 15192-4 66,823,500–67,865,000 Sahana et al. (2011)
WWT, AGW_rs43378829_4_30.8 MARBL 10013 8,553,221–50,937,899 Yokouchi et al. (2009)
YRLHT 10709 10,994,551–32,226,979 McClure et al. (2010)
MARBL 10707 10,994,551–32,226,979 McClure et al. (2010)
MHT 10712 10,994,551–32,226,979 McClure et al. (2010)
WWT 10708 10,994,551–35,086,352 McClure et al. (2010)
WWTMM 10711 19,135,469–32,226,979 McClure et al. (2010)
YWT 10710 19,135,469–32,226,979 McClure et al. (2010)
CALEASE 4655 28,268,762–35,086,352 Thomasen et al. (2008)
MARBL 1729 28,268,762–38,039,020 Mizoshita et al. (2004)
LMA 1728 28,268,762–38,039,020 Mizoshita et al. (2004)
WWT, AGW_rs109462000_11_72.4 MARBL 10909 62,118,964–82,382,031 McClure et al. (2010)
WWT_rs109028958_18_31.9 SB 11362 2,437,515–33,011,652 Seidenspinner et al. (2009)
RFI 5294 17,918,086–34,957,653 Sherman et al. (2009)
RFI 5293 17,918,086–35,720,845 Sherman et al. (2009)
WWT 11063 22,926,481–36,500,992 McClure et al. (2010)
WWT_rs42339359_29_12.3 CWT 1316 2,819,208–27,838,509 Kim et al. (2003)
CWT 1344 5,310,955–36,108,874 Casas et al. (2003)
MWT 11296 6,513,888–26,822,859 McClure et al. (2010)
TEND 1373 7,471,912–37,390,549 Casas et al. (2000)
RFI 4403-4 7,760,040–28,758,488 Nkrumah et al. (2007)
FATTH 11291 11,626,483–17,915,367 McClure et al. (2010)
MHT 11290 11,626,483–17,915,367 McClure et al. (2010)
LMA 11289 11,626,483–17,915,367 McClure et al. (2010)
MWT 11293 11,626,483–26,822,859 McClure et al. (2010)
CWT 11292 11,626,483–26,822,859 McClure et al. (2010)
WWTMM 11294 11,626,483–26,822,859 McClure et al. (2010)
YWT_rs133575890_6_68.0
YWT_rs110875592_6_68.0
YWT_rs135029160_6_68.0
YWT_ rs109300035_6_68.4
YWT_rs110545556_2_95.8
YWT_rs134262111_1_3.51
YWT_rs109532225_15_42.9 MHT 11001 29,452,266–50,231,208 McClure et al. (2010)
CALEASE 11000 36,441,038–51,210,066 McClure et al. (2010)
WWT 11002 40,819,540–51,210,066 McClure et al. (2010)
WWTMM 11003 40,819,540–51,210,066 McClure et al. (2010)
YWT_rs109419103_21_56.6
YWT_rs43538101_8_24.5 BWT 10825 15,196,699–29,543,811 McClure et al. (2010)
CWT 10826 15,196,699–29,543,811 McClure et al. (2010)
MHT 10828 24,157,132–29,543,811 McClure et al. (2010)
YRLHT 10830 24,157,132–29,543,811 McClure et al. (2010)
SB 11443 24,157,132–48,094,361 Kühn et al. (2003)
PWG_rs41566285_24_34.0 YWT 11197 30,004,563–41,590,595 McClure et al. (2010)
CALEASE 11196 30,004,563–41,590,595 McClure et al. (2010)
WWT 11198 30,004,563–41,590,595 McClure et al. (2010)
PWG_rs41569509_9_9.3 RFI 5279 5,803,533–12,440,486 Sherman et al. (2009)
WWT 10852 8,888,721–18,194,890 McClure et al. (2010)
YWT 10851 8,888,721–18,194,890 McClure et al. (2010)
MARBL 10850 8,888,721–18,194,890 McClure et al. (2010)
CALEASE 10853 8,888,721–18,194,890 McClure et al. (2010)
MARBL 4507 8,888,721–25,471,420 Imai et al. (2007)
PWG_rs42219323_16_80.1
PWG_rs41585202_24_47.1 FCR 5308 25,435,547–51,266,517 Sherman et al. (2009)
MARBL 11200 41,590,595–50,955,296 McClure et al. (2010)
1AGW = preweaning ADG; BWT = BW at birth; CALEASE = calving ease; CWT = carcass weight; FATTH = fat thickness at the 12th rib; FCR = feed conversion ratio; LMA = LM area; MARBL = marbling score; MHT = height at maturity; MWT = BW at maturity; PWG = postweaning ADG; RFI = residual feed intake; SB = stillbirth; TEND = tenderness score; WWT = BW at weaning; WWTMM = weaning weight-maternal milk; YWT = yearling BW; YRLHT = yearling height.
2ID = identification.
3Btau4.6 = bovine genome sequence assembly Btau4.6 (Elsik et al., 2015).