Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Mokry, Fabiana Barichello; Higa, Roberto Hiroshi; de Alvarenga Mudadu, Maurício; Oliveira de Lima, Andressa; Meirelles, Sarah Laguna Conceição; Barbosa da Silva, Marcos Vinicius Gualberto; Cardoso, Fernando Flores; Morgado de Oliveira, Maurício; Urbinati, Ismael; Méo Niciura, Simone Cristina; Tullio, Rymer Ramiz; Mello de Alencar, Maurício; Correia de Almeida Regitano, Luciana

doi:10.1186/1471-2156-14-47

BMC Genomic Data

Table 2 Summary of information available for the Highest 1% SNPs selected by the stepwise regression

From: Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

dbSNP¹	Chr²	Position	% dEBV³	Genes⁴in ± 250Kb	Fat-related QTL⁵	QTL reference
rs133046994	10	18129602	11.12	THSD4, LRRC49	SF, MS	[65, 66]
rs137294146	1	132385787	9.41	SOX14, CLDN18, DZP1L	FT12R, IF	[29, 71]
rs109349988	3	15814096	5.21	KCNN3, EFNA3, EFNA4, DCST2, LOC100294774, PMVK, ADAR, CHRNB2, ADAM15, ZBTB7B, LOC100294857, DCST1, FLAD1, PYGO2, CKS1B, PBXIP1, SHC1, LOC100294894	FT12R, MS	[66]
rs136717249	19	37969870	4.88	B4GALNT2, GNGT2, ABI3, PHOSPHO1, ZNF652, NGFR, PHB, IGF2BP1, GIP	OAC, PAC	[84, 85]
rs134790147	13	20780821	3.51	CCDC7, ARL5B, MGC152301, LOC100848675, LOC100847992	FT12R	[29]
rs136287610	25	42678992	2.89	FAM20C, LOC783396, LOC100300875, LOC100337322, PRKAR1B, PDGFA, PTCHD3, LOC783852, LOC783961	FT12R	[29]
rs136393667	11	65619399	2.51	LOC786621, LOC100139826, ETAA1	FT12R, MS	[29]
rs41790889	16	990255	2.07	OPTC, PRELP, FMOD, BTG2, LOC789413, LOC789394, CHI3L1, MYBPH, ADORA1, LOC100847554	FT12R, MS	[29]
rs42126516	4	52535108	1.99	TFEC, LOC100296613, TES	MS	[29, 97]
rs42021729	3	64737352	1.46		MS	[98]
rs137001098	8	95507919	1.46	SMC2, LOC100337180	MS	[29]
rs43341824	1	50110036	1.23	LOC785980, ALCAM	OAC, FT12R	[85, 99]
rs41683753	13	33219105	1.04	CACNB2, NSUN6, EPC1, LOC10084770	PAC, MS	[29, 85]
rs136348926	12	10043410	0.90	LOC786945
rs109869647	3	13195543	0.72	LOC100849046, LOC100848852, LOC784007, LOC783963	MS	[66]
rs110833507	11	42856561	0.69	LOC100296234, LOC100296682, BCL11A
rs42923911	2	12761205	0.57	LOC787311, LOC100848878
rs135638125	10	18147174	0.55	THSD4, LRRC49	MS, SF	[65, 66]
rs110607520	9	96622647	0.66	SYTL3, TULP4, TMEM181, EZR, LOC781263, DYNLT1, RSPH3, LOC782714, TAGAP, LOC782637	MS	[29]
rs110025080	9	11710300	0.52	RIMS1
rs109697559	2	61906393	0.58	LOC100847709, LOC100297008, LCT, UBXN4, MCM6, DARS, R3HDM1, MIR128-1	MS	[29]

¹ Reference SNP cluster report.
² Chromosome in B. taurus.
³ % dEBV variance is the model R² for each of the SNPs in the final analysis which fits all SNPs as fixed effects into a regression analysis.
⁴ Gene symbol.
⁵SF subcutaneous fat, FT12R fat thickness at the 12th rib, IF intramuscular fat, FT fat thickness, MS marbling score, OAC oleic acid content, PAC palmitoleic acid content.

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