德州驴体尺性状的全基因组关联分析

doi:10.11843/j.issn.0366-6964.2025.04.023

Abstract

Abstract:

To investigate the genetic basis of the body traits in Dezhou donkeys, this study collected blood samples from 139 healthy female Dezhou donkeys aged 2-3 years old as experimental materials. Body traits of the experimental population were measured, and descriptive statistical analyses were conducted. All individuals were genotyped using the 'Molbreeding Donkey No. 1' 40K liquid chip. The mixed linear model was used to perform a genome-wide association study (GWAS) on 11 body traits, and functional annotation and pathway enrichment analysis was performed on candidate genes. The fine mapping and linkage disequilibrium analyses was combined to detect the potential causal SNP loci associated with body traits. The GWAS results revealed 3 SNPs at the genome-wide significance level, 20 SNPs at the genome-wide suggestive level, and 41 candidate genes were identified as significantly associated with body traits. The GO and KEGG enrichment analysis indicated that candidate genes were significantly enriched in biological processes related to osteogenic differentiation, skeletal muscle development and lipid metabolism. Fine mapping and linkage disequilibrium analysis detected 4 significant SNPs with strong linkage disequilibrium within the candidate region on chromosome 16. The results of this study lay the foundation for the analysis of the genetic mechanism of body traits in Dezhou donkeys, and provide a reference for the application of molecular marker-assisted selection in donkey breeding.

Key words: Dezhou donkey, body traits, genome-wide association study, fine mapping

CLC Number:

S822.2

LI Cong, SU Jiangtian, LI Yidan, WANG Zhaofei, YU Jie, LEI Chuzhao, DANG Ruihua. Genome-wide Association Study of Body Traits in Dezhou Donkey[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(4): 1744-1754.

Figures/Tables 8

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性状 Trait	最大值 Max	最小值 Min	平均值±标准差 Mean±SD	变异系数/% CV
体长/cm Body length	155.00	118.00	132.17±6.86	5.19
体高/cm Withers height	151.00	117.00	138.04±6.19	4.49
头长/cm Head length	64.00	44.00	55.11±3.30	5.99
颈长/cm Neck length	82.00	55.00	69.45±4.83	6.96
胸围/cm Chest circumference	179.00	133.00	157.11±7.06	4.50
胸宽/cm Chest width	53.00	32.00	42.10±3.47	8.25
胸深/cm Chest depth	67.00	48.00	58.12±3.93	6.76
尻长/cm Hip length	49.00	35.00	40.45±2.51	6.19
尻宽/cm Hip width	52.00	36.00	43.64±2.90	6.65
尻高/cm Hip height	152.00	118.00	139.43±6.12	4.39
管围/cm Cannon circumference	21.00	13.00	15.74±1.35	8.55

性状 Trait	位点 SNP	P值 P-value	基因 Gene
体长 Body length	21:91 503 240	3.14×10^-7	ATG7, SYN2, PPARG
	20:21 286 387	2.07×10^-5	BARX2
体高 Withers height	24:23 343 731	1.60×10^-6	ASCC3, SIM1
头长 Head length	6:72 093 776	8.14×10^-6	CTNNA2
	29:35 886 892	1.44×10^-5	GJD4
	2:46 901 188	1.85×10^-5	ADGRA1, CFAP46, KNDC1
	14:15 884 941	1.98×10^-5	CLEC16A, CIITA, SOCS1
颈长 Neck length	4:83 924 683	2.54×10^-6	TSN, NIFK
	4:84 006 403	1.97×10^-5
胸宽 Chest width	16:45 878 080	8.85×10^-7	PDE4B, LEPR
胸深 Chest depth	16:29 057 786	1.90×10^-6	COL24A1, CCN1, ZNHIT6, SYDE2, DNAI3
	16:29 189 524	5.06×10^-6
	16:29 121 493	1.22×10^-5
	16:28 935 452	2.10×10^-5
	11:58 626 672	1.08×10^-5	Not found
尻长 Hip length	16:33 634 323	5.65×10^-7	Not found
	22:10 131 560	9.98×10^-6	LRIG3, SLC16A7
	27:8 494 369	1.61×10^-5	VEGFC
尻宽 Hip width	1:68 845 784	1.88×10^-6	ZNF804B, STEAP1, TEX47
	5:38 279 154	8.46×10^-6	PIK3R3, MAST2
管围	7:94 911 085	4.86×10^-6	PIK3C3
Cannon circumference	13:4 356 242	5.87×10^-6	NT5M, PEMT, FLCN, MPRIP, COPS3
	13:5 440 529	7.80×10^-6	FAM83G, GRAP, EPN2, MFAP4

性状 Trait	候选区域 Candidate region	位点 SNP	后验概率 Posterior probability
体长 Body length	20: 20 793 098-21 758 076	20:21 286 387	0.999
		20:21 467 517	0.889
	21: 91 046 592-91 929 365	21:91 503 240	0.999
		21:91 224 217	0.476
体高 Withers height	24: 22 855 789-23 775 288	24:23 595 950	1.000
		24:23 690 180	1.000
		24:23 343 731	1.000
		24:22 920 106	0.554
头长 Head length	6: 71 605 039-72 542 551	6:72 093 776	0.936
		6:72 179 511	0.352
	29: 35 388 388-36 370 323	29:35 886 892	0.999
		29:36 370 323	0.993
		29:36 314 803	0.991
	2: 46 439 788-47 286 995	2:46 901 188	0.962
	14: 15 390 407-16 379 240	14:15 884 941	0.991
		14:15 390 407	0.846
颈长 Neck length	4: 83 666 925-84 489 543	4:83 924 683	1.000
		4:84 006 403	1.000
		4:84 489 543	0.523
胸宽 Chest width	16: 45 379 140-46 335 855	16:45 878 080	0.999
		16:45 863 712	0.430
胸深 Chest depth	11: 58 128 302-59 098 496	11:58 626 672	0.994
		11:58 295 507	0.809
	16: 28 622 350-29 616 040	16:29 057 786	0.494
		16:28 622 350	0.297
尻长 Hip length	16: 33 143 130-34 132 572	16:33 634 323	0.999
		16:34 083 160	0.996
		16:33 853 810	0.399
	22: 9 664 581-10 553 415	22:10 131 560	0.974
	27: 8 024 389-8 978 857	27:8 494 369	0.968
尻宽 Hip width	1: 68 361 851-69 298 764	1:68 845 784	1.000
		1:68 640 878	0.999
		1:68 583 033	0.972
		1:68 746 075	0.869
	5: 37 815 051-38 776 904	5:38 279 154	0.994
		5:38 647 887	0.372
管围	7: 94 456 782-95 388 036	7:94 911 085	0.989
Cannon circumference	13: 3 862 146-4 807 467	13:4 356 242	0.983
	13: 4 956 846-5 919 064	13:5 440 529	0.998
		13:5 830 048	0.579
		13:5 029 534	0.613

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Genome-wide Association Study of Body Traits in Dezhou Donkey

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