狮头鹅群体遗传多样性和体重体尺全基因组关联分析

doi:10.11843/j.issn.0366-6964.2024.09.016

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (9): 3914-3924.doi: 10.11843/j.issn.0366-6964.2024.09.016

狮头鹅群体遗传多样性和体重体尺全基因组关联分析

黄红艳¹(), 张力允¹(), 黄智荣¹, 伍仲平¹, 张续勐¹, 欧阳宏佳¹, 陈俊鹏², 林桢平², 田允波¹, 李秀金¹^,*(), 黄运茂¹^,*()

1. 仲恺农业工程学院动物科技学院/广东省水禽健康养殖科技创新平台，广州 510225
2. 广东省汕头市白沙禽畜原种研究所，汕头 515821

收稿日期:2024-03-18 出版日期:2024-09-23 发布日期:2024-09-27
通讯作者: 李秀金,黄运茂 E-mail:huanghongyan@zhku.edu.cn;zhangliyun@zhku.edu.cn;lixiujin996@126.com;huangyunmao@zhku.edu.cn
作者简介:黄红艳(1995-)，男，河南开封人，硕士，主要从事水禽遗传育种研究，E-mail：huanghongyan@zhku.edu.cn
张力允(1993-)，女，辽宁大连人，硕士，主要从事水禽遗传育种研究，E-mail：zhangliyun@zhku.edu.cn
第一联系人：
黄红艳和张力允为同等贡献作者
基金资助:
广东省地方特色物种狮头鹅育种联合攻关项目(2023-XDY-00-001);广东省现代农业水禽产业技术体系创新团队(2022KJ137)

The Study on Population Genetic Diversity and Genome-wide Association Study of Body Weight and Size Traits for Lion-head Geese

Hongyan HUANG¹(), Liyun ZHANG¹(), Zhirong HUANG¹, Zhongping WU¹, Xumeng ZHANG¹, Hongjia OUYANG¹, Junpeng CHEN², Zhenping LIN², Yunbo TIAN¹, Xiujin LI¹^,*(), Yunmao HUANG¹^,*()

1. Science & Technology Innovation Platform of Guangdong Waterfowl Health Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
2. Baisha Poultry and Livestock Origin Research Institute, Shantou 515821, China

Received:2024-03-18 Online:2024-09-23 Published:2024-09-27
Contact: Xiujin LI, Yunmao HUANG E-mail:huanghongyan@zhku.edu.cn;zhangliyun@zhku.edu.cn;lixiujin996@126.com;huangyunmao@zhku.edu.cn

摘要/Abstract

摘要：

旨在探究狮头鹅群体遗传多样性和体重体尺性状全基因关联分析。本试验随机选取2年龄休产状态的狮头鹅111只(公鹅20、母鹅91只)，进行体重和体尺指标表型测定和二代基因组测序(5×)，对测序数据进行SNPs位点检测，计算狮头鹅群体遗传多样性指标，利用单标记回归混合模型开展SNPs与体重体尺性状的关联分析。本试验采用Bonferroni法校正，即全基因组水平阈值(0.05/总SNPs)和染色体水平阈值(0.05/染色体SNP数目)，确定显著性SNPs位点，并对染色体水平显著性SNPs位点上、下游50 kb进行基因注释。经过质控，共计获得7 577 552个有效SNPs用于进一步分析。群体多样性分析显示，历史有效群体含量、最小等位基因频率、多态信息含量、观察杂合度、期望杂合度和近交系数分别为234、0.25、0.34、0.26、0.34和0.22。共检测出6 164个连续纯合片段，长度在1.0~2.0 Mb的纯合片段占比最多(74.4%)。体重体尺性状的全基因组关联分析发现38个染色体水平显著性SNPs，涉及90个基因。其中影响生长发育相关的基因有7个，即D2HDH、THAP4、ESPNL、EPT1、TNPO3、MCF2L、AIP1。本研究利用二代基因组测序数据发现，狮头鹅群体存在一定程度近交现象，挖掘出与狮头鹅体重和体尺性状相关的7个候选基因，可为后续狮头鹅群体保种、功能基因研究和分子育种开展提供重要参考。

关键词: 狮头鹅, 群体多样性, 体重体尺性状, 全基因组关联分析

Abstract:

The aim of this study was to investigate the genetic diversity of Lion-head geese and to perform the genome-wide association study of body weight and size traits. In this study, the 111 lion-head geese (20 males and 91 females) were randomly selected. They are two years old and off-season. The phenotypes detection of body weight and size traits and the second-generation genome sequencing (5×) for these geese were performed. SNPs from the sequencing data was called, the genetic diversity indexes was calculated and the association between SNPs and body weight and size traits was performed using the single SNP regression mixed model. The Bonferroni correction was used, i.e., the genome-wide threshold (0.05/a total of SNPs) and the chromosome-wide threshold (0.05/number of SNPs on each chromosome) to define the significant SNPs. The gene annotation was performed based on the 50 kb upstream and downstream of chromosome-wide significant SNPs. By the quality control, a total of 7 577 552 SNPs was obtained for the further analysis. The analysis of genetic diversity found that effective population size, minor allele frequency, polymorphic information content, observed heterozygosity, expected heterozygosity and inbreeding coefficient were 234, 0.25, 0.34, 0.26, 0.34 and 0.22, respectively. A total of 6 164 runs of homozygosity was detected, the high proportion (74.4%) of which ranged from 1.0 Mb to 2.0 Mb. We found 38 chromosome-wide significant SNPs by the association between SNPs and body weight and size traits, and these significant SNPs were involved in 90 genes. Among these genes, D2HDH, THAP4, ESPNL, EPT1, TNPO3, MCF2L and AIP1 were previously reported to affect the growth and development.In this study, by using the second generation genome sequencing data, we found a certain degree of inbreeding phenomenon for the Lion-head geese population and detected 7 candidate genes affecting the body weight and size traits, which can provide important references for the subsequent conservation of the Lion-head geese, the study of gene function and the application of molecular breeding.

Key words: Lion-head goose, population genetic diversity, body weight and size traits, genome-wide association study

中图分类号:

S835.2

黄红艳, 张力允, 黄智荣, 伍仲平, 张续勐, 欧阳宏佳, 陈俊鹏, 林桢平, 田允波, 李秀金, 黄运茂. 狮头鹅群体遗传多样性和体重体尺全基因组关联分析[J]. 畜牧兽医学报, 2024, 55(9): 3914-3924.

Hongyan HUANG, Liyun ZHANG, Zhirong HUANG, Zhongping WU, Xumeng ZHANG, Hongjia OUYANG, Junpeng CHEN, Zhenping LIN, Yunbo TIAN, Xiujin LI, Yunmao HUANG. The Study on Population Genetic Diversity and Genome-wide Association Study of Body Weight and Size Traits for Lion-head Geese[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(9): 3914-3924.

图/表 8

表 1

图 1

图 2

表 2

表 3

图 3

表 4

显著性SNPs位点"

性状 Trait	染色体 Chromosome	SNPs位置 Position	功能注释 Function annotation	候选基因 Gene
体重 Body weight	5	5:2300617	内含子	ACKA
	8	8:30133648	基因间	/
	9	9:11552267	基因上游	T4S1、NEUR4、ESPNL、G3ST2、THAP4、KTHY、ATG4B、D2HDH
	20	20:10823559	内含子	CABP8
胸宽 Chest width	8	8:6837235	内含子	TT39A、EPS15
胸宽 Chest width	14	14:17266712	基因间	/
胸深 Chest depth	1	1:147040959	内含子	PCID2、LAMP1、CUL4A、MCF2L、FA10
	2	2:47791095	基因间	/
	3	3:14051391	基因间	/
	4	4:59812177	基因间	/
	5	5:17426205	基因上游	RTJK、KS6A5、TTC7B
	20	20:8724007	基因间	RFC2、NTAL、CLIP2
骨盆宽 Pelvic width	14	14:1516505	基因间	RNF14、GNPI1
	18	18:3587225	内含子	CCG4、CCG1
	30	30:1992836	基因间	OPSB
体斜长Body-slant length	2	2:44820521	基因下游	EPT1、MARE2
龙骨长 Keel length	1	1:1229901	内含子	TNPO3、SND1
	1	1:48378687	内含子	RTJK、LKHA4、HUTI、HUTH
	18	18:7043981	基因下游	OTOP3、USH1G、OTOP2、HID1、FADS6、CDR2L
颈长 Neck length	10	10:15832904	内含子	MAGI1
	10	10:20923440	基因间	/
	14	14:10667386	基因间	DUS1
	14	14:10717636	内含子	RTJK
颈围 Neck circumference	2	2:8295313	基因间	SIA4A
	2	2:72691717	内含子	AIP1、RTJK
	21	21:7325312	内含子	TPRGL、WRP73、MEGF6
	22	22:424407	内含子	CLD22、ZBT16、5HT3A、UBP28
	29	29:3363012	基因上游	RPOB、POL、FV1
	30	30:1318061	基因下游	CP2G1、CP2C2、POL、ZC11A、O14J1
胫长 Tibia length	8	8:11781946	基因间	CA210、TIE1、ELOV1、CDC20、PIF1、EBP2、CFA57
	8	8:11929974	基因间	SIA7C
	8	8:14984264	内含子	DNS2B、VIT2、RPF1、URIC
	8	8:15008813	内含子	VIT2、RPF1
	10	10:8281363	内含子	ZMY10、TM115、C56D2、NPRL2、CA2D2
	16	16:1652251	内含子	ZBT46、TPD54、DNJC5
胫围 Tibia circumference	17	17:12971390	基因上游	VP37B、APC7、HIP1R、CCD62、AT2A2、GPN3
	18	18:11564724	基因间	FHAB、SHSA6
	30	30:1234187	内含子	CP2G1、CP2C2、DCAF8、CCD81

表 4

图 4

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测定指标 Trait	样本数量/只 Number	平均值 Mean	标准差 SD	最大值 Max	最小值 Min	变异系数/% C.V
体重/kg Body weight	111	6.11	0.94	8.63	3.98	15.45
胸宽/cm Chest width	111	116.99	5.35	138.61	104.03	4.58
胸深/cm Chest depth	111	117.39	5.44	134.60	106.36	4.63
胫长/cm Tibia length	111	102.69	4.10	113.94	92.10	3.99
骨盆宽/cm Pelvic width	111	101.36	4.07	107.65	69.93	4.02
颈围/cm Neck circumference	111	12.52	1.03	15.60	11.50	8.23
颈长/cm Neck length	111	35.30	2.35	42.30	32.50	6.66
体斜长/cm Body-slant length	111	36.95	1.74	41.80	33.80	4.72
龙骨长/cm Keel length	111	18.94	1.15	22.50	16.10	6.06
胫围/cm Tibia circumference	111	6.39	0.35	7.73	5.67	5.54

遗传多样性指标 The indexes of genetic diversity	平均值±标准差 Mean±SD
有效群体含量 Effective population size(Ne)	234(13世代以前)
最小等位基因频率 Minor allele frequency(MAF)	0.25±0.13
多态信息含量 Polymorphism information content(PIC)	0.34±0.13
观察杂合度 Observed heterozygosity(Ho)	0.26±0.11
期望杂合度 Expected heterozygosity(He)	0.34±0.13
近交系数 Inbreeding coefficient(F)	0.22±0.10

ROHs片段范围/Mb The length of ROHs	ROHs片段个数 Number of ROHs	所占比例% Proportion
1.0~2.0	4 583	74.4
2.0~3.0	1 016	16.5
3.0~6.0	477	7.7
>6.0	88	1.4

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狮头鹅群体遗传多样性和体重体尺全基因组关联分析

The Study on Population Genetic Diversity and Genome-wide Association Study of Body Weight and Size Traits for Lion-head Geese

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