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

中国农业科学 ›› 2023, Vol. 56 ›› Issue (19): 3894-3904.doi: 10.3864/j.issn.0578-1752.2023.19.015

全基因组关联分析筛选鹅蛋品质相关分子标记

高广亮¹^,²(), 张克山¹^,²(), 赵献芝¹^,², 许国洋¹, 谢友慧¹^,², 周莉³, 张昌莲¹^,², 王启贵¹^,²()

¹ 重庆市畜牧科学院，重庆402460
² 重庆市肉鹅遗传改良工程技术研究中心，重庆402460
³ 重庆綦江区动物疫病预防控制中心，重庆401420

收稿日期:2022-05-10 接受日期:2023-08-08 出版日期:2023-10-01 发布日期:2023-10-08
通信作者:
王启贵，E-mail：wangqigui@hotmail.com
联系方式: 高广亮，E-mail：guanglianggaocq@hotmail.com。张克山，E-mail：zhangkshLK1988@163.com。高广亮和张克山为同等贡献作者。
基金资助:
重庆市科研机构绩效激励引导专项项目(cstc2022jxjl80007); 重庆市科研院所绩效激励引导专项项目(22527J); 财政部和农业部：国家现代农业产业技术体系(CARS-42-51); 重庆市技术创新与应用发展专项重点项目(cstc2019jscx-gksbX0097)

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

GAO GuangLiang¹^,²(), ZHANG KeShan¹^,²(), ZHAO XianZhi¹^,², XU GuoYang¹, XIE YouHui¹^,², ZHOU Li³, ZHANG ChangLian¹^,², WANG QiGui¹^,²()

¹ Chongqing Academy of Animal Science, Chongqing 402460
² Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460
³ Chongqing Qijiang Animal Disease Control Center, Chongqing 401420

Received:2022-05-10 Accepted:2023-08-08 Published:2023-10-01 Online:2023-10-08

摘要/Abstract

摘要：

【目的】通过筛选与鹅蛋品质性状相关的分子标记和候选基因，为解析蛋品质性状的遗传机制及分子标记辅助选择提供理论支撑。【方法】采用同批次健康四川白鹅群体（209只）作为研究对象。收集了每只鹅在产蛋高峰期连续生产的5枚蛋，并测定了蛋重、蛋形指数、蛋壳强度、蛋壳厚度、蛋壳重和蛋黄重量等6个蛋品质性状。基于前期209只四川白鹅（母鹅）2.896 Tb全基因组重测序数据（12.44×/个体），采用全基因组关联分析的方法，筛选与蛋品质性状相关的SNP位点和重要候选基因，并通过核酸飞行时间质谱方法检测了这些SNP位点的基因型频率。【结果】经过筛选过滤，共有9 279 339个SNPs和209个个体用于后续研究。GWAS研究发现，48个SNP位点与6个鹅蛋品质性状显著或建议性显著相关（阈值分别为5.43×10^-9和1.09×10^-7），并注释出27个蛋品质性状相关的候选基因，包括妊娠相关血浆蛋白A（pappalysin1, PAPPA）、蛋白丝氨酸/苏氨酸磷酸酶调节亚基2基因（serine/threonine-protein phosphatase 4 regulatory subunit 2，PP4R2）、乙醇胺磷酸转移酶1（ethanolamine phosphotransferase 1, EPT1）和离子型谷氨酸受体K2（glutamate receptor ionotropic, kainate 2，GRIK2）等，其中候选基因PAPPA参与蛋白质代谢，促进生长因子IGF生成，在PP4R2的11bp范围内存在5个SNPs与蛋壳厚度显著相关，另外在GRIK2上有6个SNPs与蛋黄重量显著相关，GRIK2和PP4R2分别与机体血钙维持功能以及胆固醇代谢相关。功能富集研究发现，候选基因主要参与了response to growth factor（GO:0070848）、intracellular chemical homeostasis（GO:0055082）、response to hormone（GO:0009725）和regulation of the monoatomic ion transport（GO:43269）等代谢通路。【结论】经GWAS方法筛选出PAPPA、GRIK2、ASCC3和EPT1分别作为蛋重、蛋黄重、蛋壳强度等蛋品质性状潜在功能基因，为鹅蛋品质性状的改良提供了分子遗传标记的理论参考。

关键词: 全基因组关联分析, 分子标记辅助选择, 鹅, 蛋品质性状

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

高广亮, 张克山, 赵献芝, 许国洋, 谢友慧, 周莉, 张昌莲, 王启贵. 全基因组关联分析筛选鹅蛋品质相关分子标记[J]. 中国农业科学, 2023, 56(19): 3894-3904.

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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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2023.19.015

https://www.chinaagrisci.com/CN/Y2023/V56/I19/3894

图/表 6

表1

表2

表3

筛选与蛋品质性状显著相关的SNPs表"

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

表3

图1

图2

表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

全基因组关联分析筛选鹅蛋品质相关分子标记

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

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