全基因组关联分析筛选文昌鸡体尺性状相关分子标记

doi:10.3864/j.issn.0578-1752.2024.10.015

中国农业科学 ›› 2024, Vol. 57 ›› Issue (10): 2046-2060.doi: 10.3864/j.issn.0578-1752.2024.10.015

• 畜牧·兽医 • 上一篇

全基因组关联分析筛选文昌鸡体尺性状相关分子标记

骆娜¹^,²^,³(), 安炳星³, 魏立民¹^,², 文杰³, 赵桂苹¹^,²^,³()

¹ 海南省农业科学院三亚研究院（海南省实验动物研究中心），海南三亚 572025
² 海南省农业科学院畜牧兽医研究所，海口 571100
³ 中国农业科学院北京畜牧兽医研究所/动物营养学国家重点实验室，北京 100193

收稿日期:2023-11-27 接受日期:2024-03-14 出版日期:2024-05-16 发布日期:2024-05-23
通信作者:
赵桂苹，E-mail：zhaoguiping@caas.cn
联系方式: 骆娜，E-mail：ItsLorna@163.com。
基金资助:
文昌鸡优势特色产业集群项目(WCSCICP20211106); 海南省三亚崖州湾科技项目(SKJC-2022-PTDX-002); 现代农业产业技术体系建设专项资金(CARS-41)

Identification of Molecular Markers Associated with Body Size Traits Through Genome-Wide Association Analysis in Wenchang Chickens

LUO Na¹^,²^,³(), AN BingXing³, WEI LiMin¹^,², WEN Jie³, ZHAO GuiPing¹^,²^,³()

¹ Sanya Research Institute, Hainan Academy of Agricultural Sciences, Sanya 572025, Hainan
² Institute of Animal Husbandry and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100
³ State Key Laboratory of Animal Nutrition/Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193

Received:2023-11-27 Accepted:2024-03-14 Published:2024-05-16 Online:2024-05-23

摘要/Abstract

摘要：

【目的】体尺是评价禽类生长特性的主要指标，通过筛选与文昌鸡体尺性状相关的分子标记及候选基因，为解析体尺性状的遗传机制及分子育种提供理论支撑。【方法】利用海南省文昌鸡品系3个世代（n=2 024）群体作为研究对象，测定每只鸡在上市日龄的胫长、胫围、体斜长、龙骨长及胸宽等5个体尺性状。采集血液进行鸡“京芯一号”55 K芯片测序及基因分型，使用GEMMA软件与PLINK软件进行全基因组关联分析，鉴定与体尺性状相关的SNP位点和候选基因，通过LD分析鉴定与体尺性状显著相关的单倍型。【结果】表型结果显示，113日龄文昌鸡公鸡平均胫长8.64 cm，胫围0.46 cm，体斜长19.73 cm，龙骨长12.32 cm，胸宽6.81 cm；母鸡平均胫长6.98 cm，胫围0.40 cm，体斜长17.79 cm，龙骨长10.45 cm，胸宽6.24 cm。经过质控后，共保留42 206个SNPs和2 024个个体用于后续研究。使用Plink软件进行PCA主成分分析，结果发现3个世代群体存在一定的分散情况，因此在GWAS关联分析中加入了前3个主成分作为协变量，以校正群体结构对关联分析的影响。GWAS结果研究共鉴定出19个SNPs位点与胫长性状显著或建议性显著相关（P值分别为2.17789E-06和4.35578E-05），23个SNPs位点与胫围性状显著或建议性显著相关，7个SNPs位点与体斜长性状显著或建议性显著相关，2个SNPs位点与龙骨长性状显著或建议性显著相关，未鉴定出与胸宽性状或建议性显著相关的SNPs位点。通过对显著性位点进行注释，结果共鉴定到16个体尺性状相关的候选基因，包括羧基末端 LIM 结构域结合蛋白2（LIM domain binding 2，LDB2）、染色体缩合蛋白G（non-SMC condensin I complex subunit G，NCAPG）、序列相似家族184成员B基因（family with sequence similarity 184 member B，FAM184B）、A 型钾离子通道调节蛋白4（potassium voltage-gated channel interacting protein 4，KCNIP4）等。通过LD单倍型分析结果显示，GGA4存在3个显著关联的单倍型，对于胫长性状，rs316943436和rs313978573两个位点位于单倍型区块中；对于胫围性状，rs313196946AA、rs316242963、rs315796839、rs313978573、rs734365522共5个位点位于单倍型区块中；对于体斜长性状，只有1个位点（rs313978573）位于单倍型区块中，其中候选基因LDB2和NCAPG在显著的block区块中被注释到。【结论】经GWAS方法筛选出SEPSECS、LGI2、DHX15、KCNIP4、NCAPG、FAM184B、LDB2、CC2D2A作为胫长性状潜在的候选基因；FH、TBC1D1、DTHD1、SEPSECS、LGI2、SOD3、PPARGC1A、KCNIP4、NCAPG、FAM184B、CLRN2、LDB2、TAPT1、CC2D2A作为胫围性状潜在的候选基因，KCNIP4、LDB2、TAPT1、NRXN3作为体斜长性状潜在的候选基因，FAM184B作为龙骨长性状潜在的候选基因。总之，本文确定了LDB2、NCAPG和FAM184B等作为胫长、胫围、体斜长和龙骨长等体尺性状的潜在功能基因。为文昌鸡体尺性能的分子标记辅助选择育种提供理论支撑。

关键词: 全基因组关联分析, 鸡, 体尺性状, 胫长, 胫围

Abstract:

【Objective】 Body size traits are the primary indicators for evaluating avian growth characteristics. By selecting molecular markers and candidate genes related to body size traits in Wenchang chickens, this study could provide the theoretical support for deciphering the genetic mechanisms and molecular breeding of body size traits. 【Method】 Three generations of Wenchang chicken lines in Hainan Province (n=2 024) were used in this study. Five body size traits were measured on each chicken at market age, including shank length, shank girth, body slope length, keel length, and chest width. Blood samples were collected for DNA extraction, followed by sequencing and genotyping using the "Jingxin No.1" 55 K chip. Genome-wide association analysis was conducted using GEMMA and PLINK software to identify SNP loci and important candidate genes associated with body size traits. LD analysis was performed to identify haplotypes significantly associated with body size traits. 【Result】 Phenotypic data showed that, at 113 days of age, Wenchang cockerels had average shank length of 8.64 cm, shank girth of 0.46 cm, body slope length of 19.73 cm, keel length of 12.32 cm, and chest width of 6.81 cm. Wenchang hens had average shank length of 6.98 cm, shank girth of 0.40 cm, body slope length of 17.79 cm, keel length of 10.45 cm, and chest width of 6.24 cm. After quality control, 42 206 SNPs and 2 024 individuals were retained for further analysis. PCA analysis using PLINK software revealed some dispersion among the three generations, prompting the inclusion of the top three principal components as covariates in the GWAS analysis to correct for population structure effects. The GWAS results identified 19 SNPs significantly or suggestively associated with shank length (P value=2.17789E-06/4.35578E-05), 23 SNPs associated with shank girth, 7 SNPs associated with body slope length, and 2 SNPs associated with keel length. No SNPs significantly associated with chest width were identified. Annotation of significant loci identified 16 candidate genes related to body size traits, including LDB2, NCAPG, FAM184B, and KCNIP4. LD haplotype analysis revealed 3 significant haplotypes in GGA4, with candidate genes LDB2 and NCAPG annotated in significant block loci. Regarding the shank length trait, two loci, including rs316943436 and rs313978573, were situated within the haplotype block. For shank girth, five loci, namely rs313196946AA, rs316242963, rs315796839, rs313978573, and rs734365522, were located within the haplotype block. In the case of body slope length, only one locus (rs313978573) resides within the haplotype block. 【Conclusion】 Through the GWAS method, those potential candidate genes for shank length, including SEPSECS, LGI2, DHX15, KCNIP4, NCAPG, FAM184B, LDB2, and CC2D2A, were identified. For shank girth, potential candidate genes encompassed FH, TBC1D1, DTHD1, SEPSECS, LGI2, SOD3, PPARGC1A, KCNIP4, NCAPG, FAM184B, CLRN2, LDB2, TAPT1, and CC2D2A. KCNIP4, LDB2, TAPT1, and NRXN3 were identified as potential candidate genes for body slope length, while FAM184B emerged as a potential candidate gene for keel length. In summary, this study established LDB2, NCAPG, and FAM184B as potential functional genes associated with various body size traits, providing the theoretical support for molecular marker-assisted selection in enhancing body performance in Wenchang chickens.

Key words: whole genome association analysis, chicken, body size traits, shank length, tibial circumference

骆娜, 安炳星, 魏立民, 文杰, 赵桂苹. 全基因组关联分析筛选文昌鸡体尺性状相关分子标记[J]. 中国农业科学, 2024, 57(10): 2046-2060.

LUO Na, AN BingXing, WEI LiMin, WEN Jie, ZHAO GuiPing. Identification of Molecular Markers Associated with Body Size Traits Through Genome-Wide Association Analysis in Wenchang Chickens[J]. Scientia Agricultura Sinica, 2024, 57(10): 2046-2060.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2024.10.015

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图/表 10

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表2

筛选与体尺性状显著相关的 SNPs 表"

表型 Traits	位点 SNP	染色体 Chromosome	位置 Position	等位基因 Genotype	MAF	P值 P value	解释的表型方差比例 PVE	基因 Gene symbol
胫长 Shank length	4:73548926	4	73548926	C/T	0.442	1.8E-06**	1.16	SEPSECS
	4:73571298	4	73571298	A/G	0.142	1.6E-07**	1.40	LGI2
	4:73716854	4	73716854	C/G	0.354	1.3E-08**	1.66	DHX15
	4:74769982	4	74769982	A/G	0.231	3.6E-05*	0.84	KCNIP4
	4:74837421	4	74837421	C/T	0.244	2.3E-06*	1.14	KCNIP4
	4:74928910	4	74928910	G/A	0.177	2.7E-05*	0.89	KCNIP4
	4:74937196	4	74937196	C/A	0.478	1.5E-09**	1.89	KCNIP4
	4:75796627	4	75796627	A/G	0.274	9.2E-06*	0.96	NCAPG
	4:75895966	4	75895966	G/C	0.323	1.1E-07**	1.45	NCAPG
	4:75966447	4	75966447	G/A	0.376	1.5E-11**	2.36	FAM184B
	4:76097204	4	76097204	T/C	0.08	8.6E-08**	1.46	LDB2
	4:76149397	4	76149397	A/G	0.213	1.7E-05*	0.94	LDB2
	4:76192459	4	76192459	T/A	0.274	1.7E-08**	1.64	LDB2
	4:76291739	4	76291739	T/C	0.255	3.3E-05*	0.85	LDB2
	4:76694053	4	76694053	C/G	0.211	7.7E-06*	1.02	CC2D2A
胫围 Shank girth	2:85647809	2	85647809	T/C	0.318	1.4E-05*	0.92	FH
	4:69709375	4	69709375	G/A	0.261	8.2E-07**	1.19	TBC1D1
	4:70178152	4	70178152	T/C	0.478	3.8E-05*	0.88	DTHD1
	4:73548926	4	73548926	C/T	0.443	4.0E-08**	1.58	SEPSECS
	4:73571298	4	73571298	A/G	0.142	4.7E-06*	1.08	LGI2
	4:73665546	4	73665546	A/G	0.447	1.7E-07**	1.44	SOD3
	4:73994772	4	73994772	A/G	0.319	3.2E-05*	0.90	PPARGC1A
	4:74937196	4	74937196	C/A	0.48	2.9E-09**	1.86	KCNIP4
	4:75796627	4	75796627	A/G	0.274	2.5E-08**	1.52	NCAPG
	4:75804809	4	75804809	C/T	0.21	4.5E-08**	1.47	NCAPG
	4:75966447	4	75966447	G/A	0.378	3.2E-08**	1.60	FAM184B
	4:75990543	4	75990543	T/C	0.223	8.1E-06*	1.03	CLRN2
	4:76084503	4	76084503	C/T	0.496	1.1E-05*	1.01	LDB2
	4:76192459	4	76192459	T/A	0.276	9.5E-08**	1.49	LDB2
	4:76201985	4	76201985	T/G	0.25	4.1E-07**	1.26	LDB2
	4:76291739	4	76291739	T/C	0.255	1.2E-05*	0.94	LDB2
	4:76358568	4	76358568	A/G	0.06	4.5E-07**	1.31	LDB2
	4:76473315	4	76473315	C/T	0.36	1.2E-05*	1.00	TAPT1
	4:76694053	4	76694053	C/G	0.212	4.1E-05*	0.87	CC2D2A
龙骨长Keel length	4:75966447	4	75966447	G/A	0.374	9.9E-07**	1.36	FAM184B
体斜长Body slope length	4:74769982	4	74769982	A/G	0.232	8.5E-06*	0.97	KCNIP4
	4:76192459	4	76192459	T/A	0.275	3.9E-05*	0.95	LDB2
	4:76473315	4	76473315	C/T	0.363	1.2E-06**	1.35	TAPT1
	5:39848026	5	39848026	C/G	0.069	2.8E-05*	0.95	NRXN3

表2

图5

图6

表3

图7

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体尺 Body size (cm)	性别 Sex	观测数 n	最大值 Max	最小值 Min	平均值 Mean	标准差 SD	变异系数 CV (%)
胫长 Shank length	公Male	1054	9.40	7.50	8.46	0.32	3.82
胫长 Shank length	母Female	958	7.90	6.30	6.98	0.23	3.23
胫围 Shank girth	公Male	1034	0.51	0.40	0.46	0.02	4.14
胫围 Shank girth	母Female	961	0.49	0.35	0.40	0.03	6.31
体斜长 Body slope length	公Male	1019	22.80	16.10	19.73	1.29	6.56
体斜长 Body slope length	母Female	903	20.10	16.40	17.79	0.60	3.37
龙骨长 Keel length	公Male	1012	16.60	9.80	12.32	1.18	9.56
龙骨长 Keel length	母Female	901	13.10	8.70	10.45	0.62	5.95
胸宽 Chest width	公Male	992	8.85	5.00	6.81	0.68	9.91
胸宽 Chest width	母Female	929	8.03	4.40	6.24	0.74	11.80

性状 Traits	位点 Locus	个体数 Number	平均值±标准误(基因型) Mean±SE(Genotype)			P 值 P value
胫长 Shank length	rs313196946	1965	77.58±0.67a (AA, n=152)	77.39±0.29a (AG, n=769)	77.67±0.25a (GG, n=1044)	0.770
	rs316943436	1965	77.69±0.20a (CC, n=1657)	76.83±0.45b (TC, n=302)	75.00±3.62ab (TT, n=6)	0.043
	rs313978573	1965	77.79±0.25a (AA, n=1037)	77.04±0.28b (TA, n=780)	78.58±0.58ab (TT, n=148)	0.028
胫围 Shank girth	rs313196946	1949	43.74±0.27a (AA, n=152)	43.26±0.13ab (AG, n=761)	43.02±0.11b (GG, n=1036)	0.044
	rs316242963	1949	44.42±0.36a (CC, n=88)	43.20±0.14b (CT, n=634)	43.06±0.10b (TT, n=1227)	0.002
	rs315796839	1949	42.97±0.17a (CC, n=472)	43.04±0.12a (CT, n=986)	43.62±0.16b (TT, n=491)	0.007
	rs313978573	1949	43.39±0.11a (AA, n=1023)	42.87±0.13b (TA, n=778)	43.24±0.29ab (TT, n=148)	0.0066
	rs734365522	1949	43.02±0.11a (GG, n=1093)	43.27±0.13a (TG, n=749)	44.02±0.34b (TT, n=107)	0.019
体斜长 Body slope length	rs313978573	1877	18.91±0.05a (AA, n=987)	18.65±0.05b (TA, n=746)	18.88±0.12ab (TT, n=144)	0.0017

全基因组关联分析筛选文昌鸡体尺性状相关分子标记

Identification of Molecular Markers Associated with Body Size Traits Through Genome-Wide Association Analysis in Wenchang Chickens

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