新疆地方鸡遗传关系和基因组差异研究

doi:10.11843/j.issn.0366-6964.2026.01.014

摘要/Abstract

摘要：

旨在揭示拜城油鸡、和田鸡和吐鲁番鸡等3种新疆地方鸡相互之间的遗传关系和基因组差异，从而在基因组层面为新疆地方鸡遗传资源的保护与开发提供科学依据。本研究以65份鸡的全基因组重测序数据为对象，借助Rstudio、Plink、Pedstats等软件对数据实施过滤处理；通过状态同源（identical by state，IBS）多维标度分析不同鸡种的群体遗传结构，利用Treemix及Dsuite开展基因渗入（gene introgression）分析，采用群体间单倍体扩增纯合性检测（cross population extended haplotype homozygosity，XP-EHH）及跨群体的符合似然比检验（cross population composite likelihood radio test，XP-CLR）挖掘选择信号。数据质控后，10 228 705个常染色体的单核苷酸多态位点（single nucleotide polymorphism，SNP）用于基因渗入和选择信号的研究，4 657 217个最小等位基因频率（minor allele frequency，MAF）≥0.2的常染色体SNPs则被用来进行遗传关系分析。群体遗传关系分析显示，拜城油鸡和吐鲁番鸡的遗传距离最远，遗传分化系数达到（genetic differentiation coefficient，F_ST）0.077 7，和田鸡与拜城油鸡及吐鲁番鸡的遗传距离较近，F_ST分别为0.053 5和0.056 3。且和田鸡与吐鲁番鸡之间存在一次基因渗入，渗入信号最强的区域位于4号染色体，该区域包含ABLIM2等与耐热性能相关的基因。而在拜城油鸡与吐鲁番鸡的选择信号分析中，共筛选出70个参与关键生物学进程的候选基因。其中，CLCN6、ACTA2、CRIM1、IARS2等基因可能与耐热性能相关；BNIP2、DTNA、RAB3GAP2等基因可能涉及肌肉生长调控；AGMO、TSNARE1等基因则可能与斗鸡攻击性行为的形成有关。研究清晰地揭示了新疆3种地方鸡种之间存在的遗传关系，发现了和田鸡与吐鲁番鸡之间存在的基因组渗入区域及相关基因，鉴定了拜城油鸡和吐鲁番鸡之间的基因组选择区域及其中包括的与耐热性、肌肉生长、斗鸡攻击性行为等特色性状相关的候选基因，从而为新疆地方鸡种特色性状的保护和利用提供分子依据。

关键词: 全基因组重测序, 鸡, 遗传结构, 基因渗入, 选择信号

Abstract:

This study aimed to reveal the genetic relationships and genomic differences among 3 Xinjiang local chicken breeds including Baicheng-You chickens， Hetian chickens， and Tulufan chickens， so as to provide references for the protection and utilization of genetic resources of local domestic chickens in Xinjiang at the genomic level. The research took 65 chickens whole-genome resequencing datasets as the research objects and utilized softwares such as Rstudio， Plink， and Pedstats to filter the data. The population genetic structure of different chicken breeds was analyzed through identical by state （IBS） multi-dimensional scaling. Gene infiltration analysis was carried out using Treemix and Dsuite. The selection signals were mined by using the cross population extended haplotype homozygosity （XP-EHH） and cross population composite likelihood radio test （XP-CLR） methods. After filtering， a total of 10 228 705 autosomal single nucleotide polymorphisms （SNPs） were obtained for analyzing the introgression and selection signals， while 4 657 217 autosomal SNPs with minor allele frequency （MAF）≥0.2 were used for genetic relationship analysis. The results of genetic relationship showed that the genetic distance between Baicheng-You and Tulufan chickens was farthest， and their genetic differentiation coefficient （F_ST） was 0.077 7， while the genetic distance between Hetian and Baicheng-You， Tulufan chickens were close and the F_ST was 0.053 5 and 0.056 3， respectively. Furthermore， there was an introgression event between Hetian and Tulufan chickens. The highest score of introgression region located in the chromosome 4， which contained some genes associated with heat tolerance， such as ABLIM2. While selection signals analysis between Baicheng-You and Tulufan chickens identified 70 candidate genes involved in important biological processes. Among them， genes such as CLCN6， ACTA2， CRIM1， and IARS2 might be related to the heat resistance performance； Genes such as BNIP2， DTNA， and RAB3GAP2 might be involved in the regulation of muscle growth； Genes such as AGMO， TSNARE1 might be related to the formation of aggressive behavior in cockfighting. The research clearly revealed the genetic relationships among 3 local chicken breeds in Xinjiang， discovered the genomic infiltration regions and related genes between the Hetian and Tulufan chickens， and identified the genomic selection regions between the Baicheng-You and Tulufan chickens and the candidate genes related to characteristic traits such as heat tolerance， muscle growth， and aggressive behavior of fighting chickens. Thus providing molecular basis for the protection and utilization of the characteristic traits of chicken breeds in Xinjiang.

Key words: whole genome resequencing, chickens, genetic structure, gene introgression, selection signal

中图分类号:

S831.2

杨凯, 李东锋, 邵勇钢, 翟曼君, 白现广, 张立凡. 新疆地方鸡遗传关系和基因组差异研究[J]. 畜牧兽医学报, 2026, 57(1): 155-166.

YANG Kai, LI Dongfeng, SHAO Yonggang, ZHAI Manjun, BAI Xianguang, ZHANG Lifan. Study on Genetic Relationships and Genomic Differences of Local Chicken Breeds in Xinjiang[J]. Acta Veterinaria et Zootechnica Sinica, 2026, 57(1): 155-166.

图/表 9

图1

图2

图3

表1

图4

图5

表2

拜城油鸡与吐鲁番鸡差异区域间部分与重要生物学过程相关的基因"

染色体 Chromosome	基因位置 Gene position		基因 Gene	功能 Function
1	34535707	34549257	HELB	牛的环境适应性（Environmental adaptability of cattle）^［31］
1	67188237	67209122	KRAS	牛骨骼肌生成（Bovine skeletal myogenesis）^［32］
2	11439678	11481488	PFKP	参与鸡的体细胞重编程过程（Participate in the process of somatic reprogramming of chickens）^［33］
2	27838091	28021352	AGMO	斗鸡攻击性行为（Aggressive behavior of gamecock chickens）^［34］
2	107360212	107534708	DTNA	鸡肌肉发育（Muscle development in chickens）^［35］
2	118477237	118542230	CRISPLD1	人类心力衰竭（Human heart failure）^［36］
2	146916969	147397126	TSNARE1	斗鸡情绪调节和神经系统发育相关（Emotion regulation and nervous system development of gamecock chickens）^［37］
3	18846742	18887139	RAB3GAP2	调节人肌纤蛋白分泌（Regulate myocilin secretion of human）^［38］
3	18886888	18911956	IARS2	调节人血管生成（Regulates human angiogenesis）^［39］
3	32394497	32555854	CRIM1	人冠状血管内皮细胞发育（Coronary vascular endothelial cell development of human）^［40］
6	19118047	19156066	ARHGAP22	鼠上调节肌动蛋白细胞骨架（Regulates actin cytoskeleton of mice）^［41］
6	20062668	20118932	ACTA2	鸡羽毛更新循环（Cycle of chicken feather renewal）^［42］
7	11545922	11578947	ALS2	人肌萎缩侧索硬化（Amyotrophic lateral sclerosis of human）^［43］
10	5823812	5839785	BNIP2	调节人成肌细胞分化（Regulate the differentiation of human myoblast）^［44］
10	7185220	7263560	MYO1E	抑制小鼠破骨细胞分化（Suppresses osteoclast differentiation of mice）^［45］
13	4953827	5426056	SLIT3	促进鸡细胞肌源性分化（Promote myogenic differentiation of chicken cells）^［46］
21	5586241	5605153	CLCN6	小鼠血管平滑肌收缩力（Vascular smooth muscle contractility of mice）^［47］

表2

图6

图7

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区域排名 Region ranking	区域位置 Region position		染色体 Chromosome	基因位置 Gene position		基因 Gene
1	80624337	81362351	4	80649049	80786524	ABLIM2
1	80624337	81362351	4	80793977	80825261	SH3TC1
1	80624337	81362351	4	80855311	80877258	HTRA3
1	80624337	81362351	4	80933353	80968494	ACOX3
1	80624337	81362351	4	80968536	80981295	TRMT44
1	80624337	81362351	4	81142872	81147963	GPR78
1	80624337	81362351	4	81163250	81197855	CPZ
2	80690000	81424671	4	81401297	81403526	SOHO-1
2	80690000	81424671	4	81409978	81412649	HMX1
3	80492569	81115546	4	79986601	80511445	SORCS2
3	80492569	81115546	4	80530710	80589183	AFAP1
6	115118700	115583816	2	115110507	115125929	VXN
6	115118700	115583816	2	115139370	115162145	MYBL1
6	115118700	115583816	2	115177217	115191152	VCPIP1
6	115118700	115583816	2	115207256	115264028	SGK3
6	115118700	115583816	2	115277568	115277646	SNORD87
6	115118700	115583816	2	115280942	115286441	TCF24
6	115118700	115583816	2	115289879	115308471	PPP1R42
6	115118700	115583816	2	115315596	115326952	COPS5
6	115118700	115583816	2	115379044	115463018	ARFGEF1
6	115118700	115583816	2	115482232	115569184	CPA6
8	4797296	5576303	11	4645274	4873781	FTO
8	4797296	5576303	11	4878175	4936909	RPGRIP1L
8	4797296	5576303	11	4976046	4988616	AKTIP
8	4797296	5576303	11	4991886	5011381	RBL2
8	4797296	5576303	11	5015742	5089734	CHD9
8	4797296	5576303	11	5176684	5176790	U6
8	4797296	5576303	11	5223979	5345307	TOX3
10	65570685	66428389	1	65833774	66173568	SOX5
11	115230557	115708914	2	115620395	115787873	PREX2
13	80802442	81599620	4	81576968	81578308	ADRA2C
14	65645081	66496818	1	66453732	66480164	ETNK1
17	115318072	115835589	2	115821712	115984273	C8orf34
19	23676537	24481736	1	23662850	23926311	KCND2
19	23676537	24481736	1	24435899	24484038	ANKRD26
20	115041718	115539645	2	115081599	115082672	RRS1