全基因组关联分析筛选鹅蛋品质相关分子标记

doi:10.3864/j.issn.0578-1752.2023.19.015

Abstract

Abstract:

【Objective】 The objective of this study was to screen molecular markers and candidate genes related to goose egg quality traits, to provide a theoretical support for the analysis of the genetic mechanism of egg quality traits and marker-assisted selection. 【Method】 In this study, a batch of healthy Sichuan White Geese (209 individuals) was selected as the research subjects. Five eggs from each goose during the peak egg production period were collected, and then six egg quality traits were measured, including egg weight, egg shape index, eggshell strength, eggshell thickness, eggshell weight, and egg yolk weight. Based on the whole-genome resequencing data (2.896 Tb, 12.44×/individual) of 209 Sichuan White Geese (female geese), a genome-wide association analysis was conducted to identify SNP loci and important candidate genes associated with egg quality traits. The genotype frequencies of the SNP loci were determined using the nucleic acid flight time mass spectrometry method. 【Result】After filtering, a total of 9 279 339 SNPs and 209 individuals were included for further analysis. The GWAS analysis identified 48 SNP loci significantly or suggestively associated with six egg quality traits (thresholds: 5.43×10^-9 and 1.09×10^-7). These loci were annotated to 27 candidate genes related to egg quality traits, including Pregnancy-associated plasma protein A (PAPPA), Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PP4R2), Ethanolamine phosphotransferase 1 (EPT1), and Glutamate receptor ionotropic, kainate 2 (GRIK2). Among them, the candidate gene PAPPA was involved in protein metabolism and promotes the generation of insulin-like growth factor. Five SNPs within the 11 bp range of PP4R2 were significantly associated with eggshell thickness. Additionally, six SNPs on the GRIK2 gene were significantly associated with yolk weight. GRIK2 and PP4R2 were respectively associated with blood calcium homeostasis and cholesterol metabolism in organisms. Functional enrichment analysis revealed that the candidate genes were mainly annotated to “response to growth factor” (GO:0070848), “intracellular chemical homeostasis” (GO:0055082), “response to hormone” (GO:0009725), and “regulation of monoatomic ion transport” (GO:43269). 【Conclusion】 The GWAS analysis showed that the PAPPA, GRIK2, ASCC3, and EPT1 are potential functional genes associated with various egg quality traits, such as egg weight, egg yolk weight, and shell strength, providing theoretical references for molecular genetic marker-assisted selection of goose egg quality traits.

Key words: genome-wide association analysis, molecular marker-assisted selection, goose, egg quality traits

GAO GuangLiang, ZHANG KeShan, ZHAO XianZhi, XU GuoYang, XIE YouHui, ZHOU Li, ZHANG ChangLian, WANG QiGui. Identification of Molecular Markers Associated with Goose Egg Quality Through Genome-Wide Association Analysis[J].Scientia Agricultura Sinica, 2023, 56(19): 3894-3904.

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Figures/Tables 6

Table 1

Table 2

Table 3

The candidate SNPs that were significantly associated with egg quality traits"

表型 Traits	SNP	染色体 Chromosome	位置 Position	等位基因 Genotype	P 值 P value	基因 Gene symbol
蛋重 Egg weight	chr29:3653854	29	3653854	G/A	6.98×10^-09**	PAPPA
蛋重 Egg weight	chr15:24022773	15	24022773	G/T	3.04×10^-08*	ADA2C
蛋重 Egg weight	chr29:3648283	29	3648283	T/C	3.98×10^-08*	SGCE
蛋重 Egg weight	chr12:32856792	12	32856792	G/C	4.00×10^-08*	TXNL1
蛋形指数 Egg shape index	chr4:20222331	4	20222331	A/T	5.76×10^-09**	BCOR
蛋形指数 Egg shape index	chr4:20222337	4	20222337	G/T	5.76×10^-09**	BCOR
蛋形指数 Egg shape index	chr4:20186649	4	20186649	C/G	8.11×10^-09**	BCOR
蛋形指数 Egg shape index	chr15:14494772	15	14494772	A/G	2.39×10^-08*	M1IP1
蛋形指数 Egg shape index	chr9:32698552	9	32698552	T/A	3.32×10^-08*	GLRX3
蛋形指数 Egg shape index	chr15:14497223	15	14497223	T/C	4.48×10^-08*	DHX15
蛋形指数 Egg shape index	chr15:20262147	15	20262147	T/G	4.60×10^-08*	TBC1D14
蛋形指数 Egg shape index	chr15:14786356	15	14786356	C/A	5.15×10^-08*	DHX15
蛋形指数 Egg shape index	chr15:14494538	15	14494538	A/G	6.81×10^-08*	DHX15
蛋形指数 Egg shape index	chr9:32698542	9	32698542	C/G	9.67×10^-08*	DHX15
蛋壳强度 Eggshell strength	chr1:444834	1	444834	G/A	5.70×10^-09**	DTNB
蛋壳强度 Eggshell strength	chr1:1466542	1	1466542	A/T	2.27×10^-08*	EPT1
蛋壳强度 Eggshell strength	chr1:1467878	1	1467878	T/C	5.45×10^-08*	EPT1
蛋壳强度 Eggshell strength	chr5:429465	5	429465	G/A	6.09×10^-08*	NFAC1
蛋壳强度 Eggshell strength	chr5:429561	5	429561	G/A	6.24×10^-08*	NFAC1
蛋壳强度 Eggshell strength	chr5:429586	5	429586	G/A	1.89×10^-08*	NFAC1
蛋壳强度 Eggshell strength	chr5:20299054	5	20299054	T/C	3.04×10^-08*	DC1I1
蛋壳强度 Eggshell strength	chr5:20324779	5	20324779	T/A	2.93×10^-08*	DC1I1
蛋壳强度 Eggshell strength	chr5:20325470	5	20325470	C/T	3.72×10^-08*	DC1I1
蛋壳强度 Eggshell strength	chr18:6281804	18	6281804	A/G	1.53×10^-08*	BSN
蛋壳强度 Eggshell strength	chr19:1292936	19	1292936	T/C	1.38×10^-08*	NOX5
蛋壳强度 Eggshell strength	chr37:3102113	37	3102113	A/G	7.03×10^-08*	KANL1
蛋壳重Eggshell weight	chr18:8947937	18	8947937	T/C	1.35×10^-09*	K1257
蛋壳重Eggshell weight	chr6:21095706	6	21095706	C/T	1.81×10^-08*	CP4V2
蛋壳重Eggshell weight	chr10:33758926	10	33758926	A/G	2.05×10^-08*	KI16B
蛋壳重Eggshell weight	chr10:33758927	10	33758927	A/G	2.05×10^-08*	KI16B
蛋壳重Eggshell weight	chr1:11330934	1	11330934	A/G	3.29×10^-08*	TRIB2
蛋壳重Eggshell weight	chr4:36821594	4	36821594	A/G	8.42×10^-08*	GBRB3
蛋壳重Eggshell weight	chr33:1028855	33	1028855	T/C	9.79×10^-08*	K1522
蛋壳厚度Eggshell width	chr18:18353514	18	18353514	T/C	3.54×10^-09*	PP4R2
蛋壳厚度Eggshell width	chr18:18353504	18	18353504	C/T	4.94×10^-08*	PP4R2
蛋壳厚度Eggshell width	chr18:18353509	18	18353509	G/A	4.94×10^-08*	PP4R2
蛋壳厚度Eggshell width	chr18:18353511	18	18353511	A/G	4.94×10^-08*	PP4R2
蛋壳厚度Eggshell width	chr18:18353515	18	18353515	C/G	4.94×10^-08*	PP4R2
蛋黄重量 Egg yolk weight	chr1:36803702	1	36803702	C/T	4.53×10^-08*	ASCC3
蛋黄重量 Egg yolk weight	chr1:36829464	1	36829464	A/G	3.46×10^-08*	ASCC3
蛋黄重量 Egg yolk weight	chr1:37042051	1	37042051	G/A	9.08×10^-08*	GRIK2
蛋黄重量 Egg yolk weight	chr1:37047532	1	37047532	C/T	7.13×10^-08*	GRIK2
蛋黄重量 Egg yolk weight	chr1:37246474	1	37246474	G/C	3.68×10^-08*	GRIK2
蛋黄重量 Egg yolk weight	chr1:37262254	1	37262254	C/T	5.03×10^-08*	GRIK2
蛋黄重量 Egg yolk weight	chr1:37282181	1	37282181	G/A	2.87×10^-09*	GRIK2
蛋黄重量 Egg yolk weight	chr1:37295041	1	37295041	A/G	9.54×10^-08*	GRIK2
蛋黄重量 Egg yolk weight	chr11:26886902	11	26886902	C/T	6.17×10^-08*	ELOC
蛋黄重量 Egg yolk weight	chr34:3206857	34	3206857	A/G	9.35×10^-08*	SOX13

Table 3

Fig. 1

Fig. 2

Table 4

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位置 SNP position	上游扩增引物 Upstream amplification primer	下游扩增引物 Downstream amplification primer	单碱基延伸探针 Single-base extension probe
chr29:3653854	TGGTTCCACAGTTGAGAATG	GTACCGAACTCAAGTAGAGC	gggaCACAGTTGAGAATGTGAACA
chr15:24022773	GGGAATTTCCCAAACAGGGC	ACCAGCACCTTGACAACAGC	ccaCTCACCCCAGGTGCTTGGTCA
chr12:32856792	AGGCAATAACATGTGGACGG	GCCAATTTCTAACCAGAAGG	gGCTGAAAAGTGTTGTCTGTAAG
chr15:20262147	TGGCAGCCGCGTATTTACC	TGAAGGAGGGCGGCTTTCAT	cccctCGTATTTACCGATCGCAG
chr1:444834	CCATTCTACGATCTAGGCTG	CCCTCAGAATGTCCTATACC	TGATGATTCTAGATTCACAAGG
chr18:6281804	AGTGCTTAGCAAGGCTCAAC	CGATGACAGGATTTCCAACC	aAAGGCTCAACCCCCTGGC
chr1:1466542	TTTCCACATCTCCAAGTGCC	CTCAAGTGCCACGTCTTAAC	ggtgTTTCCTCTCCACCATCCCAGTAT
chr5:20299054	CAGCAGCATTTGTTCTCACC	GCATGACTTCTGCAGTTACG	ACAACTACAGCATGCTGAT
chr1:1467878	TGGAAAAGGCCCTTTCCAAG	GCTTTTCCCCCCTCTTTTAG	GCCCTTTCCAAGACGGGTG
chr1:11330934	CCCGTGTTGTTTACGAGTTC	TTACAAATAGGCTTCGCATC	CAGTATACATCATATTAAGAAGTCAT
chr18:18353514	ACAGTGAGAGGTGAATGGAG	TAGGCAACAGCTCCAACTAC	gAACTGTCTGAAAACGTAAG
chr1:36829464	GGAATTCTGTGGTACCTGTC	AGGTATCTCTATGCCAAGTC	gAGGATTGTAGTATACTGTTAACATT
chr34:3206857	GCACACTCCCACGGTATTC	TGGCTCCTGTCTCTCCTTG	CTCCCACGGTATTCACGCTC

表型 Traits	数量 Number	平均值 Mean	标准差 STDV	最大值 Maximum	最小值 Minimum	变异系数 CV（%）
蛋重 Egg weight (g)	207	132.20	18.90	166.23	87.01	0.14
蛋形指数 Egg shape index	207	1.45	0.15	1.60	1.24	0.10
蛋壳强度 Eggshell strength ( kg·cm^-2)	208	67.20	10.19	78.45	24.57	0.15
蛋壳重Eggshell weight (g)	208	22.87	3.17	32.88	14.58	0.14
蛋壳厚度Eggshell width (cm)	208	0.42	0.06	0.56	0.26	0.14
蛋黄重量 Egg yolk weight (g)	208	41.20	6.73	62.75	27.60	0.16

性状 Traits	最小二乘均值±标准差 Least-squares means ± Standard deviation (Genotype)			P值 P value
蛋重 Egg weight (g)
chr29:3653854	133.50±1.45a(AA)	119.76±2.87b(AG)	121.92±6.79b(GG)	<.0001
chr15:24022773	133.21±1.44a(GG)	124.91±2.38b(GT)	133.35±1.07a(TT)	<.0001
chr12:32856792	133.53±1.05a(CC)	118.54±3.11b(CG)	74.94±10.08c(GG)	<.0001
蛋形指数 Egg shape index
chr15:20262147	1.45±0.0047a(GG)	1.42±0.0094b(GT)	1.37±0.0347b(TT)	0.0013
蛋壳强度 Eggshell strength (g/cm³)
chr1:444834	68.85±0.74a(AA)	62.74±1.23b(GA)	53.69±4.53b(GG)	<.0001
chr18:6281804	68.41±0.65a(GG)	56.53±1.76b(GA)		<.0001
chr1:1466542	53.13±3.69c(AA)	63.41±1.24b(AT)	68.83±0.74a(TT)	<.0001
chr5:20299054	68.60±0.71a(CC)	60.79±1.40b(CT)	64.00±60.43ab(TT)	<.0001
chr1:1467878	68.75±0.70a(CC)	61.60±1.42b(CT)	54.85±3.66c(TT)	<.0001
蛋壳重量Eggshell weight (g)
chr1:11330934	24.45±0.55a(AA)	23.44±2.07ab(GA)	22.67±0.22b(GG)	0.0123
蛋壳厚度Eggshell width (mm)
chr18:18353514	0.43±0.0039a(CC)	0.38±0.01b(CT)	0.38±0.0267b(TT)	0.0001
蛋黄重量 Egg yolk weight (g)
chr1:36829464	44.92±1.79a(AA)	43.70±0.79a(GA)	39.48±0.54b(GG)	<.0001
chr34:3206857	48.58±3.61a(AA)	44.11±1.61b(GA)	40.27±0.49c(GG)	0.0077

Identification of Molecular Markers Associated with Goose Egg Quality Through Genome-Wide Association Analysis

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