全基因组关联分析筛选大别山牛体重体尺性状相关分子标记

doi:10.11843/j.issn.0366-6964.2026.01.016

Abstract

Abstract:

The objective of this study was to identify molecular marker loci and candidate genes associated with body weight and size traits in Dabieshan cattle， thereby elucidating their genetic mechanisms. A total of 515 healthy Dabieshan cattle aged between 30 and 36 months were selected， phenotypic measurements of eight traits were performed， including body weight， withers height， body slanting length， chest circumference，abdominal circumference， cannon bone circumference，hucklebone width， and hip width. Genotyping was performed using the Neogen 100K SNP chip， and a genome-wide association study （GWAS） was conducted using a mixed linear model （MLM）. The results revealed 44 single nucleotide polymorphisms （SNPs） loci significantly associated with body weight and size traits， which were annotated to 426 candidate genes. Among these， 6 candidate genes （WFIKKN2， MMP2， MATN1， PUM1， VKORC1， and VKORC1L1） related to muscle development， chondrogenesis， and bone metabolism were of particular interest. Functional enrichment analysis using Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） further indicated that the VKORC1 and VKORC1L1 genes are involved in key biological processes such as vitamin K metabolism， which warrants further investigation. In conclusion， the findings of this study provide clear molecular targets and valuable insights for the genetic improvement of the Dabieshan cattle.

Key words: Dabieshan cattle, SNP, body weight and size traits, whole-genome association study

CLC Number:

S823.2

ZHANG Liu, LI Qian, ZHAO Shuanping, JIN Hai, LI Qinggang, ZHANG Huibin, DU Xinyi, JIN Sihua, ZHU Yong, ZHAO Keqin, XU Lei, WANG Shujuan. Identification of Molecular Markers Associated with Body Weight and Size Traits through Genome-Wide Association Study in Dabieshan Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2026, 57(1): 181-193.

Figures/Tables 8

Table 1

Fig.1

Fig.2

Fig.3

Fig.4

Table 2

Information of significant loci"

表型 Phenotype	染色体Chromosome	SNP	位置 Locus	等位基因 Allele	P值 P-value	基因 Gene
体重 Bodyweight	25	25_32065350	32065350	C/A	6.06E-06
体重 Bodyweight	18	18_24729491	24729491	G/A	7.04E-06	CES5A、BREH1、NUP93、SLC12A3、HERPUD1、NLRC5、PSME3IP1、RSPRY1、AMFR、GNAO1、CPNE2
十字部高 Withersheight	20	20_48820669	48820669	A/G	3.61E-06	CDH10
十字部高 Withersheight	20	20_48932728	48932728	G/A	3.92E-06	CDH10
体斜长 Bodyslantinglength	10	10_36957819	36957819	A/G	3.39E-09	ITPKA、U6、DLL4、CHAC1、CHP1、OIP5、NUSAP1、RTF1、RPAP1、MAPKBP1、PLA2G4B、SPTBN5、PLA2G4E、INO80、NDUFAF1、TYRO3、MGA、JMJD7、EHD4、EXD1
	21	21_42348918	42348918	A/G	7.89E-07	GPR33、U6、Vault、G2E3、COCH、HECTD1、HEATR5A、ARHGAP5、SCFD1、STRN3、AP4S1、NUBPL、AKAP6
	12	12_45904326	45904326	T/A	1.42E-06	DACH1
	14	14_38755533	38755533	G/A	1.59E-06	CRISPLD1、HNF4G
	1	1_139763834	139763834	A/C	2.02E-06	U6、B3GALT5、HMGN1、GET1、LCA5L、BRWD1、SH3BGR、IGSF5、PCP4、DSCAM
	20	20_16951836	16951836	T/A	7.62E-06	U6、DIMT1、IPO11、KIF2A
胸围 Chestcircum-ference	22	22_19495134	19495134	G/A	8.79E-10	GRM7
	13	13_33911044	33911044	A/G	4.62E-09	ARHGAP12、ZEB1、ZNF438
	14	14_14274197	14274197	A/G	1.62E-08	LRATD2、U6
	16	16_51927028	51927028	C/A	1.93E-08	RNF223、ISG15、HES4、NOC2L、TMEM82、U6、TTLL10、AGRN、PERM1、SAMD11、ZBTB17、FBLIM1、SLC25A34、PLEKHM2、AGMAT、DNAJC16、CASP9、CTRC、EFHD2、KAZN、KLHL17、SPEN、CELA2A、FHAD1、TMEM51、C16H1orf159
	16	16_51949929	51949929	G/A	3.73E-08	RNF223、ISG15、HES4、NOC2L、TMEM82、U6、TTLL10、AGRN、PERM1、SAMD11、ZBTB17、FBLIM1、SLC25A34、PLEKHM2、AGMAT、DNAJC16、CASP9、CTRC、EFHD2、KAZN、KLHL17、SPEN、CELA2A、FHAD1、TMEM51、C16H1orf159
	6	6_58539931	58539931	C/A	1.59E-07	RPL9、TLR10、FAM114A1、WDR19、KLB、LIAS、SMIM14、UBE2K、TLR6、TMEM156、KLHL5、RFC1、UGDH、PDS5A
	14	14_13955770	13955770	A/G	2.69E-07	LRATD2、U6
	10	10_94086276	94086276	A/G	2.83E-07	WDR36
	2	2_37903309	37903309	G/A	6.46E-07	U12、U6、DAPL1、UPP2、CCDC148、PKP4
	6	6_86551834	86551834	A/G	1.62E-06	UTP3、GRSF1、MOB1B、DCK、GC、RUFY3、SLC4A4
	13	13_34005489	34005489	C/A	1.67E-06	ARHGAP12、ZEB1、ZNF438
	19	19_16265564	16265564	G/A	1.81E-06	CCL1、CCL8、CCL11、CCL2、U6、U4、ASIC2
	16	16_41118210	41118210	A/G	2.53E-06	TNFSF18、SNORA59A、TNFSF4、AADACL4、TNFRSF1B、TNFRSF8、DHRS3、VPS13D
	16	16_51796918	51796918	G/A	3.59E-06	RNF223、ISG15、HES4、NOC2L、TMEM82、UTTLL10、AGRN、PERM1、SAMD11、ZBTB17、FBLIM1、SLC25A34、PLEKHM2、AGMAT、DNAJC16、CASP9、CTRC、EFHD2、KAZN、KLHL17、SPEN、CELA2A、FHAD1、TMEM51、C16H1orf159
	29	29_1207110	1207110	A/G	3.99E-06	SNORD5、SNORA8、SNORD6、SNORA25、HEPHL1、VSTM5、MED17、C29H11orf54、TAF1D、CEP295、SMCO4、DEUP1、SLC36A4
	25	25_33092922	33092922	G/A	4.03E-06	RFC2、TMEM270、CLDN、CLDN3、ABHD11、DNAJC30、VPS37D、TBL2、7SK、TRIM50、NSUN5、U6、CCL26、CCL24、TMEM120A、HSPB1、RCC1L、GTF2IRD2、GTF2I、GTF2IRD1、CLIP2、LAT2、EIF4H、LIMK1、METTL27、BUD23、MLXIPL、BCL7B、FZD9、FKBP6、RHBDD2、STYXL1、MDH2、SRRM3、YWHAG、SSC4D、NCF1、ELN、BAZ1B、HIP1、POR、STX1A
	10	10_95545955	95545955	G/A	4.07E-06
	11	11_12841755	12841755	A/C	4.95E-06	U6、CYP26B1、EXOC6B、DYSF、ZNF638、PAIP2B
	15	15_50327842	50327842	G/A	5.02E-06	OR52E1、OR52J3D、OR51P1、OR51L1C、OR51P1B、OR51L1B、U6、OR51H9B、OR51H5、OR51S1B、OR51A8、OR52R1E、OR51F1B、OR51F5C、OR51F5B、OR51F23D、OR51E2、OR51A25、OR51A57、OR51E1、OR51D1、OR52I1B、OR52I1、OR52I11、OR52M2、OR52K1、OR52M1、OR52P2、OR51R1、OR52B3、OR52B4C、OR52B4K、OR51G2、TRIM68、TRIM68、OR51A49
	21	21_41411828	41411828	G/A	6.78E-06	SNORA62、GPR33、U6、Vault、G2E3、COCH、HECTD1、HEATR5A、ARHGAP5、ARHGAP5、STRN3、AP4S1、NUBPL、AKAP6
	10	10_102180727	102180727	A/G	7.45E-06	PSMC1、TDP1、KCNK13、NRDE2、CALM1、TTC7B、RPS6KA5
	22	22_33101195	33101195	A/G	7.92E-06	TAFA4、TAFA1
	28	28_26472060	26472060	A/G	8.71E-06	AIFM2、SAR1A、PPA1、LRRC20、NODAL、PRF1、TBATA、MACROH2A2、EIF4EBP2、PALD1、ADAMTS14、SGPL1、COL13A1
	11	11_12860734	12860734	A/G	9.50E-06	U6、CYP26B1、EXOC6B、DYSF、ZNF638、PAIP2B
腹围 Abdominalcircum-ference	18	18_23256421	23256421	A/G	1.43E-11	IRX5，IRX6，MMP2
腹围 Abdominalcircum-ference	19	19_35683912	35683912	A/T	5.67E-06	TOB1、WFIKKN2、ANKRD40CL、DHRS7B、TMEM11，KCNJ12、UTP18、NME2、NME1、LUC7L3、ABCC3，CACNA1G，EPN3、MAP2K3、MBTD1、ANKRD40、SPATA20、SPAG9
坐骨端宽Hucklebonewidth	21	21_42348918	42348918	A/G	1.18E-08	GPR33、U6、G2E3、COCH、HECTD1、HEATR5A、ARHGAP5、SCFD1、STRN3、AP4S1、NUBPL、AKAP6
	1	1_139763834	139763834	A/C	3.57E-07	U6、B3GALT5、HMGN1、GET1、LCA5L、BRWD1、SH3BGR、IGSF5、PCP4、DSCAM
	5	5_28112145	28112145	C/A	2.16E-06	SMIM41、ATG101、ANKRD33、FIGNL2、U6、CELA1、DAZAP2、KRT7、KRT80、NR4A1、TAMALIN、ACVR1B、ACVRL1、SCN8A、BIN2、SMAGP、TFCP2、GALNT6、POU6F1、SLC4A8
	20	20_12736223	12736223	T/A	2.36E-06
	25	25_33933997	33933997	A/G	6.93E-06	RFC2、TMEM270、CLDN4、CLDN3、ABHD11、DNAJC30、VPS37D、TBL2、7SK、TRIM50、NSUN5、U6、CCL2、CCL24、TMEM120、HSPB1、RCC1、GTF2IRD2、GTF2I、GTF2IRD1、CLIP2、LAT2、EIF4H、LIMK1、METTL27、BUD23、MLXIPL、BCL7B、FZD9、FKBP6、RHBDD2、STYXL1、MDH2、SRRM3、YWHAG、SSC4D、NCF1、ELN、BAZ1B、HIP1、POR、STX1A
腰角宽 Hip width	10	10_12252829	12252829	A/G	4.06E-09	KBTBD13、U5、PTGER2、SPG21、MTFMT、SLC51B、RASL12、PDCD7、CLPX、IGDCC3、DPP8、INTS14、SLC24A1、RAB11A、UBAP1L、PARP16、IGDCC、HACD3、DENND4A
	2	2_122442807	122442807	G/A	4.80E-07	SNORA70、HCRTR1
	8	8_5938128	5938128	G/A	8.18E-07	HMGB2、SAP30、HAND2、U6、SCRG1、GALNT7
	8	8_5955286	5955286	G/A	1.13E-06	HMGB2、SAP30、HAND2、U6、SCRG1、GALNT7
	25	25_27502658	27502658	A/G	1.42E-06	CTF2、ORAI3、HSD3B7、STX4、ZNF646、VKORC1、KAT8、PRSS36、FUS、PYCARD、TRIM72、COX6A2、ARMC5、SLC5A2、AHSP、OR7A53、OR7A153、ZNF713、CCT6A、SUMF2、CHCHD2、NUPR2、ASL、FBXL19、SETD1A、ZNF668、PRSS53、BCKDK、PRSS8、ITGAM、ITGAD、TGFB1I1、SEPTIN14、NIPSNAP2、PSPH、PHKG1、VKORC1L1、PHKG1、STX1B、RUSF1、MRPS17、GUSB
	12	12_9967477	9967477	A/G	1.99E-06
	1	1_152507074	152507074	G/A	4.40E-06	EAF1、COLQ、HACL1、BTD、SH3BP5、METTL6、ANKRD28
	19	19_11684567	11684567	A/G	8.87E-06	TBX2、INTS2、TBX4、BRIP1、BCAS3、CCL1

Table 2

Fig.5

Fig.6

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表型 Phenotype	样本量 Number	平均值 Mean	标准差 SD	最大值 Max	最小值 Min	变异系数/% CV
体重/kg Body weight	341	290.31	53.95	445	168	18.58
十字部高/cm Withers height	488	113.87	6.42	132.5	95	5.64
体斜长/cm Body slanting length	493	128.59	10.00	158	100	7.78
胸围/cm Chest circumference	487	159.36	12.85	197	122	8.07
腹围/cm Abdominal circumference	488	188.67	16.61	236	147	8.80
管围/cm Cannon bone circumference	321	16.12	1.15	20	13	7.15
坐骨宽/cm Hucklebone width	488	17.48	3.73	29	10	21.31
腰角宽/cm Hip width	491	37.96	4.36	49	26	11.49

Identification of Molecular Markers Associated with Body Weight and Size Traits through Genome-Wide Association Study in Dabieshan Cattle

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