龙岩山麻鸭蛋品质性状的全基因组关联研究

doi:10.3864/j.issn.0578-1752.2023.03.014

Abstract

Abstract:

【Objective】Single nucleotide polymorphisms (SNPs) and candidate genes for egg quality traits in duck were identified through genome-wide association study (GWAS) technology, so as to provide reference for molecular breeding to improve egg quality traits of Longyan Shan-Ma Duck.【Method】Egg quality traits of 235 female Longyan Shan-Ma Duck were measured, including egg weight (EW), egg shaped index (ESI), eggshell thickness (EST), eggshell strength (ESS), eggshell colour L* (ESCL), a* (ESCA), b* (ESCB), albumin height (AH), Haugh unit (HU), egg yolk colour (EYC), egg yolk weight (EYW), and egg yolk percentage relative to egg weight (EYP). Genetic parameters of these traits were estimated using multi-trait animal model by ASReml-R 4.1 software. Blood genomic DNAs of these ducks were genotyped using genotyping-by-sequencing (GBS) technology. The GWAS between egg quality traits of the late laying period and SNPs were performed. 【Result】 The heritability of EW, ESI, EST, ESL, ESA and AU was higher among the egg quality traits of Longyan Shan-Ma Duck, and ranged from 0.21 to 0.70. There was a strong positive genetic correlation (r_g= 0.91±0.37) between EW and AU, a strong negative genetic correlation (r_g= -0.98±1.03) between ESI and EYC. EST had a positive phenotypic correlation (r_p= 0.41±0.06) with ESS, negative genetic and phenotypic correlations with ESA (r_g= -0.86±0.25 and r_p= -0.15±0.07), and positive genetic and phenotypic correlations with ESB (r_g= 0.96±0.37 and 0.18±0.07). There were negative genetic and phenotypic correlations between ESA and ESB (r_g= -0.64±0.28 and r_p= -0.31±0.06). Results from the GWAS showed that seven SNPs were significantly associated with ESI, EST and yolk color (YC) at 5% Bonferroni-corrected genome-wide significance level (P<4.74×10^-6), involving six candidate genes. One SNP, chr20:11135563: G:C, was associated with ESI, which was in leucine rich repeat containing 75A gene, located on chromosome 20. Two SNPs, chr13:5766560:A:G and chrZ:968819:C:T, were associated with EST, which were located on chromosome 13, downstream 6.86 Kb of LOC106014427 and in transcription factor 4 gene, respectively. Four SNPs were associated with EYC, one SNP chr2: 38155965:G:A in potassium voltage-gated channel subfamily H member 8 gene located on chromosome 2; three SNPs located on chromosome 9, two SNPs, chr9:22623156:G:A and chr9:22623155:T:C, in insulin receptor substrate 1 gene, and one SNP, chr9:22490158:A:T, in LOC106018641 gene. Eighty-one SNPs associated with egg quality traits reached at suggestive genome-wide significance level (P<9.48×10^-5) were also found. Thirteen SNPs associated with YC were distributed in the 0.84 Mb (22.16-23.00 Mb) region of chromosome 9.【Conclusion】In this study, genetic parameters of egg quality traits of Longyan Shan-Ma Duck were estimated. Seven significant SNPs, six candidate genes, and one candidate region affecting ESI, EST and EYC traits were identified through GWAS. The findings from the present study provided a reference for the molecular breeding of egg quality traits in Longyan Shan-Ma Duck.

Key words: Longyan Shan-Ma Duck, egg quality traits, genetic parameter, SNPs, GWAS

SUN YanFa, WU Qiong, LIN RuLong, CHEN HongPing, GAN QiuYun, SHEN Yue, WANG YaRu, XUE PengFei, CHEN FeiFan, LIU JianTao, ZHOU ChenXin, LAN ShiShi, PAN HaoZhe, DENG Fan, YUE Wen, JIANG XiaoBing, LI Yan. Genome-Wide Association Study of Egg Quality Traits in Longyan Shan-Ma Duck[J].Scientia Agricultura Sinica, 2023, 56(3): 572-586.

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Figures/Tables 9

Table 1

Table 2

Table 3

Fig. 1

Table 4

Table 5

SNPs significance at genome-wise level suggestive significant association"

性状 Trait	染色体 Chromosome	标记号 SNP ID	物理位置 Position (bp)	A1 A1	BETA值 BETA	P值 P value	最近的基因 Nearest gene
蛋重EW	2	chr2:10782468:A:G	10782468	G	3.45	2.81×10^-5	U 120.07 kb ADARB2
	2	chr2:10790319:T:C	10790319	T	3.31	5.81×10^-5	U 112.21 kb ADARB2
	5	chr5:5547457:T:C	5547457	T	2.89	3.36×10^-5	U 63.45 kb MIS18BP1
	5	chr5:5547530:A:G	5547530	G	2.80	6.33×10^-5	U 63.38 kb MIS18BP1
蛋形指数ESI	3	chr3:81386471:A:G	81386471	A	-0.05	6.66×10^-5	D 13.01 NT5E
	5	chr5:7009743:G:A	7009743	G	0.06	2.77×10^-5	within CDKL1
	15	chr15:11227397:T:C	11227397	C	0.05	6.39×10^-5	within AXIN1
	15	chr15:11227409:G:A	11227409	A	0.05	7.59×10^-5	within AXIN1
	15	chr15:13294556:C:T	13294556	T	0.05	2.39×10^-5	within UBN1
	15	chr15:13395347:A:G	13395347	A	0.05	3.49×10^-5	within LOC101799012
	15	chr15:14536844:G:A	14536844	A	0.05	1.02×10^-5	U 41.78 kb RBFOX1
	16	chr16:2579629:A:T	2579629	T	-0.04	5.07×10^-5	within EP400
	16	chr16:3098786:G:A	3098786	A	-0.04	1.97×10^-5	D 22.42 kb LOC110352440
	25	chr25:6315960:T:C	6315960	C	-0.06	5.29×10^-5	D 26.17 kb LOC106020386
蛋壳厚度EST	2	chr2:22513511:C:A	22513511	A	0.03	2.51×10^-5	within ZNF804B
	2	chr2:22582514:A:G	22582514	G	0.03	4.43×10^-5	within ZNF804B
	2	chr2:22582670:G:A	22582670	A	0.03	6.51×10^-5	within ZNF804B
	6	chr6:7192663:G:A	7192663	A	0.03	6.46×10^-5	U 18.98 kb KCNK18
	6	chr6:12756206:T:A	12756206	A	0.02	7.06×10^-5	within SH3PXD2A
	12	chr12:140915:T:A	140915	A	-0.02	9.44×10^-5	within THSD4
	12	chr12:198263:G:A	198263	A	-0.02	5.31×10^-5	within THSD4
	13	chr13:5721234:C:T	5721234	T	0.02	7.27×10^-5	within LOC106014427
	19	chr19:4873329:A:G	4873329	G	0.02	2.69×10^-5	within LOC113845541
蛋壳强度ESS	5	chr5:33699890:A:T	33699890	T	0.66	6.76×10^-5	within LOC113843881
蛋壳颜色L*值 ESCL	7	chr7:3182113:T:A	3182113	A	-3.45	6.81×10^-5	within CTR9
	7	chr7:3204268:G:A	3204268	A	-3.31	6.08×10^-5	U 0.65 kb EIF4G2
	7	chr7:3204312:A:G	3204312	G	-3.34	6.05×10^-5	U 0.60 kb EIF4G2
	7	chr7:3223217:A:G	3223217	G	-3.55	1.05×10^-5	U 14.01 kb LOC113844171
	7	chr7:3223320:T:A	3223320	A	-3.37	9.92×10^-6	U 13.91 kb LOC113844171
	14	chr14:9802965:A:G	9802965	G	2.04	5.95×10^-5	within CLINT1
蛋壳颜色a*值 ESCA	1	chr1:160744676:G:C	160744676	G	-1.09	9.13×10^-5	D 3.53 kb PHF5A
	1	chr1:174907611:C:T	174907611	T	-0.89	5.86×10^-5	U 19.87 kb GPR85
	4	chr4:6332903:C:G	6332903	G	-0.93	5.91×10^-5	U 6.34 kb MANBA
	8	chr8:10668874:C:A	10668874	A	-0.97	8.83×10^-5	D 3.43 kb LOC113844346
蛋壳颜色 b*值 ESCB	1	chr1:59043295:C:T	59043295	T	-1.54	7.39×10^-5	U 142.06 kb ARHGEF7
	1	chr1:59706095:T:C	59706095	C	1.03	6.95×10^-5	D 3.76 kb COL4A2
	3	chr3:16497369:T:C	16497369	C	-1.19	2.36×10^-5	U 13.30 kb VSX1
	4	chr4:7424076:C:G	7424076	G	1.83	6.35×10^-5	within RAP1GDS1
	8	chr8:33254427:C:T	33254427	T	1.20	3.93×10^-5	within SLC30A7
蛋白高度AU	2	chr2:102420094:T:G	102420094	G	-0.89	5.83×10^-5	U 14.46 kb RBBP8
	4	chr4:5482597:A:C	5482597	C	1.49	4.59×10^-5	D 21.57 kb LOC106017184
	4	chr4:71726051:A:G	71726051	G	0.90	2.81×10^-5	within LOC106017926
	7	chr7:7414460:C:T	7414460	T	0.80	3.39×10^-5	D 1.45 kb LOC106019248
	20	chr20:6093764:T:C	6093764	T	1.30	4.41×10^-5	U 5.58 kb SGSM2
	20	chr20:10720431:A:G	10720431	G	1.01	3.37×10^-5	U 15.28 kb RTN4RL1
哈氏单位HU	1	chr1:111329343:T:C	111329343	C	12.09	8.38×10^-5	within TAGLN3
	4	chr4:75257160:A:C	75257160	A	-8.15	3.42×10^-5	U 91.88 kb LOC110353528
	7	chr7:7414460:C:T	7414460	T	6.42	5.32×10^-5	D 1.45 kb LOC106019248
	20	chr20:6093764:T:C	6093764	T	10.22	8.41×10^-5	U 5.58 kb SGSM2
	20	chr20:10720431:A:G	10720431	G	8.18	4.19×10^-5	U 15.28 kb RTN4RL1
蛋黄颜色EYC	1	chr1:196541696:G:T	196541696	T	0.75	5.41×10^-5	within CAMK1D
	2	chr2:2433073:A:G	2433073	G	0.94	2.65×10^-5	within GJC2
	2	chr2:37584936:A:G	37584936	G	1.01	1.99×10^-5	D 60.71 kb SATB1
	2	chr2:37585118:C:T	37585118	T	0.77	6.42×10^-5	D 60.53 kb SATB1
	2	chr2:57679783:T:C	57679783	C	0.71	6.82×10^-5	within GLI3
	2	chr2:57679906:A:G	57679906	G	0.70	9.04×10^-5	within GLI3
	2	chr2:115153719:T:C	115153719	C	-0.97	5.50×10^-5	within ZNF521
	2	chr2:115178457:C:T	115178457	T	-1.10	5.57×10^-5	within ZNF521
	3	chr3:51410494:C:T	51410494	T	-0.80	5.15×10^-5	within RMND1
	3	chr3:51410551:A:G	51410551	G	-0.80	5.15×10^-5	within RMND1
	6	chr6:6402767:G:A	6402767	A	-0.85	8.86×10^-5	within CACUL1
	7	chr7:10854039:A:G	10854039	G	-1.28	6.98×10^-5	within MAP2
	9	chr9:22162962:T:G	22162962	G	-1.08	4.62×10^-5	within NYAP2
	9	chr9:22163003:A:G	22163003	G	-1.07	5.51×10^-5	within NYAP2
	9	chr9:22163123:T:C	22163123	C	-1.07	5.51×10^-5	within NYAP2
	9	chr9:22490118:C:T	22490118	C	-0.96	6.18×10^-6	within LOC106018641
	9	chr9:22490249:A:G	22490249	A	-0.83	2.13×10^-5	within LOC106018641
	9	chr9:22628656:T:C	22628656	C	-0.97	5.97×10^-5	within IRS1
	9	chr9:22636905:C:T	22636905	T	-1.04	4.55×10^-5	within IRS1
	9	chr9:22798030:T:C	22798030	C	-0.92	1.94×10^-5	within COL4A3
	9	chr9:22841648:T:C	22841648	C	-0.95	6.18×10^-5	within COL4A3
	9	chr9:23005131:A:G	23005131	G	-1.04	7.05×10^-5	within DAW1
	14	chr14:1139032:G:A	1139032	A	-0.90	2.55×10^-5	within ZIC4
	24	chr24:3527498:A:G	3527498	A	0.74	7.73×10^-5	within EPB41
蛋黄重EYW	2	chr2:2865193:A:G	2865193	A	-2.66	6.56×10^-5	U 2.17 kb SEC22C
	9	chr9:11219039:A:G	11219039	G	2.15	9.42×10^-5	within TP63
	9	chr9:11360616:G:A	11360616	A	2.27	4.28×10^-5	within TP63
	9	chr9:11360684:A:G	11360684	G	2.27	4.43×10^-5	within TP63
蛋黄比例EYP	2	chr2:129285222:C:T	129285222	T	-6.95	6.53×10^-5	within RMDN1
	5	chr5:8855150:G:A	8855150	A	5.41	6.83×10^-5	D 19.17 kb LOC110352963
	6	chr6:708965:T:C	708965	C	6.13	2.71×10^-5	within DPYSL4

Table 5

Fig. 2

Fig. 3

Fig. 4

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性状 Trait	例数 N	平均值 Mean	最小值 Min	最大值 Max	标准差 SD	变异系数 CV（%）
蛋重EW (g)	235	69.70	51.30	84.30	5.28	7.57
蛋形指数ESI	235	1.33	1.15	1.50	0.06	4.52
蛋壳厚EST (mm)	235	0.33	0.20	0.44	0.04	10.68
蛋壳强度ESS (kg·cm^-2)	233	3.40	0.61	6.00	1.04	30.68
蛋壳颜色L* 值ESCL	235	78.11	65.11	86.29	2.86	3.67
蛋壳颜色a*值ESCA	234	-3.04	-8.44	-0.53	1.52	-50.17
蛋壳颜色b*值ESCB	234	4.81	1.37	13.63	1.66	34.58
蛋白高度 AH (mm)	235	6.36	1.32	20.80	3.33	9.85
哈氏单位HU	235	74.84	38.22	95.47	10.70	14.29
蛋黄颜色EYC	235	7.37	3.00	13.00	1.22	16.52
蛋黄重 EYW (g)	232	24.14	11.70	37.30	3.70	15.33
蛋黄比例 EYP (%)	232	34.77	17.06	57.91	5.52	15.87

	蛋重 EW	蛋形指数 ESI	蛋壳厚 EST	蛋壳强度 ESS	*蛋壳颜色L值 ESCL**	*蛋壳颜色a值 ESCA**	*蛋壳颜色b值 ESCB**	蛋白高度 AH	哈氏单位 HU	蛋黄颜色 EYC	蛋黄重 EYW	蛋黄比例 EYP
蛋重 EW	0.21± 0.16	-	-	-	-	-	-	0.91± 0.37*	-	-	-	-
蛋形指数 ESI	-	0.29± 0.17	-	-	-	-	-	-	-	-0.98± 1.03*	-	-
蛋壳厚 EST	-	-	0.41± 0.17	-	-	-0.86± 0.25**	0.96± 0.37**	-	-	-	-	-
蛋壳强度 ESS	-	-	0.41± 0.06***	0.01± 0.10	-	-	-	-	-	-	-	-
蛋黄颜色L*值 ESCL	-	-	-	-	0.37± 0.18	-	-	-	-	-	-	-
蛋黄颜色a*值 ESCA	-	-0.16± 0.07*	-0.15± 0.07**	-	0.25± 0.07***	0.70± 0.20	-0.64± 0.28*	-	-	-	-	-
蛋黄颜色b*值 ESCB	-	-	0.18± 0.07**	0.18± 0.06*	-0.31± 0.06***	-0.31± 0.06***	0.16± 0.14	-	-	-	-	-
蛋白高度 AH	0.04± 0.07*	-	-	0.20± 0.06**	-	-0.09± 0.07*	-	0.24± 0.18	-	-	-	-
哈氏单位 HU	-0.18± 0.07***	-	-	0.22± 0.06**	-	-0.12± 0.07*	-	-	0.08± 0.14	-		-
蛋黄颜色 EYC	-0.10± 0.07*	0.07± 0.06*	-	-	-	-	-	-	0.18± 0.06**	0.07± 0.14	-	-
蛋黄重 EYW	0.24± 0.06***	-	-	-	-	-	-	-	-	-	0.01± 0.12	-
蛋黄比例 EYP	-0.26± 0.06***	-	-	-	-	-	-	-	-	-	0.87± 0.02***	0.08± 0.12

Genome-Wide Association Study of Egg Quality Traits in Longyan Shan-Ma Duck

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染色体 Chromosome	SNPs数量 No. of SNPs	独立SNPs数量 No. of independent SNPs	染色体 Chromosome	SNPs数量 No. of SNPs	独立SNPs数量 No. of independent SNPs
1	9911	1523	16	1132	172
2	7488	1250	17	30	9
3	6116	988	18	1420	230
4	4026	644	19	989	149
5	4252	706	20	1546	251
6	2311	435	21	1382	242
7	2120	335	22	1072	177
8	2479	402	23	278	63
9	2163	407	24	687	122
10	1242	202	25	974	186
11	2177	369	26	134	48
12	1028	152	27	819	189
13	2066	377	28	766	173
14	1607	307	29	506	80
15	1545	240	Z	440	119
总计Total				62706	10547

性状 Trait	染色体 Chromosome	标记号 SNP ID	物理位置 Position (bp)	A1 A1	BETA值 BETA	P值 P value	最近的基因 Nearest gene
蛋形指数ESI	20	chr20:11135563:G:C	11135563	C	-0.05	1.48×10^-6	within LRRC75A
蛋壳厚EST	13	chr13:5766560:A:G	5766560	A	0.02	1.36×10^-6	6.86 kb D LOC106014427
蛋壳厚EST	Z	chrZ:968819:C:T	968819	T	-0.02	1.96×10^-6	within TCF4
蛋黄颜EYC	2	chr2:38155965:G:A	38155965	A	1.05	1.97×10^-6	within KCNH8
	9	chr9:22490158:A:T	22490158	T	-0.97	3.77×10^-6	within LOC106018641
	9	chr9:22623155:T:C	22623155	C	-0.92	1.91×10^-6	within IRS1
	9	chr9:22623156:G:A	22623156	A	-1.08	8.75×10^-7	within IRS1

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