广东黑鸽群体遗传结构解析及基于全基因组关联分析的黑羽性状相关变异位点验证

doi:10.16288/j.yczz.26-139

遗传 ›› 2026, Vol. 48 ›› Issue (10): 1012-1024.doi: 10.16288/j.yczz.26-139

广东黑鸽群体遗传结构解析及基于全基因组关联分析的黑羽性状相关变异位点验证

周煜博¹(), 林树带¹, 郭劲¹, 彭苏城¹, 廖增广¹, 麻芷婕¹, 顾丽红², 张丽¹()

¹ 广东海洋大学滨海农业学院，湛江 524088
² 海南省农业科学院畜牧兽医研究所，海口 571199

收稿日期:2026-06-11 修回日期:2026-09-10 出版日期:2026-09-11 发布日期:2026-09-11
通讯作者: 张丽，博士，教授，研究方向：家禽遗传育种和遗传资源。E-mail: zhangli761101@163.com
作者简介:周煜博，硕士研究生，专业方向：家禽遗传育种和遗传资源。E-mail: 18285163114@163.com
基金资助:
浙江省全省畜禽生物育种重点实验室开放课题(202501);校企合作项目(2022-5-17);海南省重点研发计划项目(ZDYF2025XDNY080)

Population genetic structure analysis of Guangdong Black pigeon and validation of black plumage trait-associated loci based on genome-wide association study

Yubo Zhou¹(), Shudai Lin¹, Jing Guo¹, Sucheng Peng¹, Zengguang Liao¹, Zhijie Ma¹, Lihong Gu², Li Zhang¹()

¹ College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
² Institute of Animal Husbandry and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China

Received:2026-06-11 Revised:2026-09-10 Published:2026-09-11 Online:2026-09-11
Supported by:
Open Project of Zhejiang Provincial Key Laboratory of Livestock and Poultry Biological Breeding(202501);University-Enterprise Cooperation Project(2022-5-17);Key Research and Development Program of Hainan Province(ZDYF2025XDNY080)

摘要/Abstract

摘要：

羽色是家禽品种鉴定的关键表型特征之一，解析其遗传基础对种质资源的保护与可持续利用具有重要意义。本研究对127只广东黑鸽和12只塔里木鸽进行全基因组重测序(whole-genome resequencing，WGR)，并整合其他4个鸽种已有的重测序数据(共40只)，通过主成分分析、群体结构分析和系统进化树构建发现，广东黑鸽遗传背景独特，与白羽及灰羽鸽群存在明显分化。进一步利用全基因组关联分析(genome-wide association study，GWAS)，经过过滤筛选后共得到1,598个单核苷酸多态性(single-nucleotide polymorphism，SNP)位点和97个插入/缺失(insertion/deletion，InDel)位点，这些位点集中分布于4号染色体内皮素B型受体亚型(endothelin receptor type B2，EDNRB2)基因及其邻近区域。本研究从该区域挑选显著性较高的3个SNP位点和2个InDel位点进行Sanger测序验证，结果显示：白羽鸽所有位点均为野生型，广东黑鸽全部位点均为突变纯合型或杂合型，说明这些变异位点的基因型与黑羽表型高度一致。本研究结果为解析广东黑鸽羽色形成的分子机制、开展分子标记辅助育种提供了可靠的候选标记。

关键词: 广东黑鸽, 羽色, 全基因组关联分析, 分子标记

Abstract:

Plumage color is one of the key phenotypic traits for breed identification in poultry, and deciphering its genetic basis is of great significance for the conservation and sustainable utilization of germplasm resources. In this study, we performed whole-genome resequencing (WGR) on 127 Guangdong Black pigeons and 12 Tarim pigeons, and integrated existing resequencing data from four other pigeon breeds (40 individuals in total). Principal component analysis, population structure analysis, and phylogenetic tree construction revealed that Guangdong Black pigeons have a unique genetic background and are clearly differentiated from white- and gray-feathered pigeon populations. We further conducted a genome-wide association study (GWAS), and after filtering and screening, identified a total of 1,598 single-nucleotide polymorphisms (SNPs) and 97 insertions/deletions (InDels). These loci were predominantly clustered in the endothelin receptor type B2 (EDNRB2) gene on chromosome 4 and in its flanking regions. From this region, we selected three highly significant SNPs and two InDels for Sanger sequencing validation. The results showed that all tested loci in white-feathered pigeons were wild-type, whereas in Guangdong Black pigeons they were either homozygous mutant or heterozygous, indicating that the genotypes at these variant loci are highly consistent with the black plumage phenotype. Our results provide reliable candidate markers for elucidating the molecular mechanism underlying plumage color formation in Guangdong Black pigeons and for implementing molecular marker-assisted breeding.

Key words: Guangdong Black pigeon, plumage color, genome-wide association study, molecular marker

周煜博, 林树带, 郭劲, 彭苏城, 廖增广, 麻芷婕, 顾丽红, 张丽. 广东黑鸽群体遗传结构解析及基于全基因组关联分析的黑羽性状相关变异位点验证[J]. 遗传, 2026, 48(10): 1012-1024.

Yubo Zhou, Shudai Lin, Jing Guo, Sucheng Peng, Zengguang Liao, Zhijie Ma, Lihong Gu, Li Zhang. Population genetic structure analysis of Guangdong Black pigeon and validation of black plumage trait-associated loci based on genome-wide association study[J]. Hereditas(Beijing), 2026, 48(10): 1012-1024.

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参考文献 28

[1]	van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet, 2014, 30(9): 418-426. pmid: 25108476
[2]	Shastry BS. SNPs: impact on gene function and phenotype. Methods Mol Biol, 2009, 578: 3-22. pmid: 19768584
[3]	Chen SF, Zhou YQ, Chen YR, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 2018, 34(17): i884-i890. pmid: 30423086
[4]	Kendig KI, Baheti S, Bockol MA, Drucker TM, Hart SN, Heldenbrand JR, Hernaez M, Hudson ME, Kalmbach MT, Klee EW, Mattson NR, Ross CA, Taschuk M, Wieben ED, Wiepert M, Wildman DE, Mainzer LS. Sentieon DNASeq variant calling workflow demonstrates strong computational performance and accuracy. Front Genet, 2019, 10: 736. pmid: 31481971
[5]	Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol, 1990, 215(3): 403-410. pmid: 2231712
[6]	Yin LL, Zhang HH, Tang ZS, Xu JY, Yin D, Zhang ZW, Yuan XH, Zhu MJ, Zhao SH, Li XY, Liu XL. rMVP: a memory-efficient, visualization-enhanced, and parallel- accelerated tool for genome-wide association study. Genomics Proteomics Bioinformatics, 2021, 19(4): 619-628. pmid: 33662620
[7]	Pla P, Alberti C, Solov'eva O, Pasdar M, Kunisada T, Larue L. Ednrb2 orients cell migration towards the dorsolateral neural crest pathway and promotes melanocyte differentiation. Pigment Cell Res, 2005, 18(3): 181-187. pmid: 15892714
[8]	Maclary ET, Shapiro MD. Widespread variation in EDNRB2 is associated with diverse melanin loss phenotypes across avian species. Mol Biol Evol, 2025, 42(11): msaf267. pmid: 41092453
[9]	Kanai SM, Clouthier DE. Endothelin signaling in development. Development, 2023, 150(24): dev201786. pmid: 38078652
[10]	Nataf V, Lecoin L, Eichmann A, Le Douarin NM. Endothelin-B receptor is expressed by neural crest cells in the avian embryo. Proc Natl Acad Sci USA, 1996, 93(18): 9645-9650. pmid: 8790384
[11]	Woolfe A, Mullikin JC, Elnitski L. Genomic features defining exonic variants that modulate splicing. Genome Biol, 2010, 11(2): R20. pmid: 20158892
[12]	Chang CM, Coville JL, Coquerelle G, Gourichon D, Oulmouden A, Tixier-Boichard M. Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens. BMC Genomics, 2006, 7: 19. pmid: 16457736
[13]	Kerje S, Lind J, Schütz K, Jensen P, Andersson L. Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. Anim Genet, 2003, 34(4): 241-248. pmid: 12873211
[14]	Zhao HM, Sun ZY, Lu HZ, Wang L, Wang SS, Zhang T. SNPs identification of MC1R gene and correlation analysis of feather color in three different feather color chicken. J Domest Anim Ecol, 2021, 42(5): 26-32.
	赵浩名, 孙志阳, 路宏朝, 王令, 王珊珊, 张涛. 3种不同羽色鸡MC1R基因SNPs鉴定及羽色相关性分析. 家畜生态学报, 2021, 42(5): 26-32.
[15]	Li JY, Bed'hom B, Marthey S, Valade M, Dureux A, Moroldo M, Péchoux C, Coville JL, Gourichon D, Vieaud A, Dorshorst B, Andersson L, Tixier-Boichard M. A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome structure. Pigment Cell Melanoma Res, 2019, 32(3): 381-390. pmid: 30457703
[16]	Gunnarsson U, Kerje S, Bed'hom B, Sahlqvist AS, Ekwall O, Tixier-Boichard M, Kämpe O, Andersson L. The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10. Pigment Cell Melanoma Res, 2011, 24(2): 268-274. pmid: 21210960
[17]	Kinoshita K, Akiyama T, Mizutani M, Shinomiya A, Ishikawa A, Younis HH, Tsudzuki M, Namikawa T, Matsuda Y. Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w)) and mottled (mo) plumage phenotypes in the chicken. PLoS One, 2014, 9(1): e86361. pmid: 24466053
[18]	Peng SC, Zhang L, Ali S, Lin SD, Liao ZG, Peng QQ, Xie PP, Zhang ZH. Whole genome resequencing uncovers candidate genes related toplumage color in Yuexi frizzled feather chicken. Poult Sci, 2025, 104(11): 105680. pmid: 40840286
[19]	Yu WH, Wang C, Xin QW, Li SJ, Feng YP, Peng XL, Gong YZ. Non-synonymous SNPs in MC1R gene are associated with the extended black variant in domestic ducks (Anas platyrhynchos). Anim Genet, 2013, 44(2): 214-216. pmid: 37107611
[20]	Zhang XY, Zhu T, Wang L, Lv XZ, Yang WF, Qu CQ, Li HY, Wang HE, Ning ZH, Qu LJ. Genome-wide association study reveals the genetic basis of duck plumage colors. Genes (Basel), 2023, 14(4): 856. pmid: 22591010
[21]	Guo QX, Jiang Y, Wang ZX, Bi YL, Chen GH, Bai H, Chang GB. Genome-wide analysis identifies candidate genes encoding feather color in ducks. Genes (Basel), 2022, 13(7): 1249. pmid: 35886032
[22]	Yang YZ, Wang HY, Li GQ, Liu Y, Wang C, Qiu SY, Wang XZ, Yao JF, Zhu LH, He DQ. Using comparative genomics to detect mutations regulating plumage variations in graylag (A. anser) and swan geese (A. cygnoides). Gene, 2022, 834: 146612. pmid: 35618220
[23]	Wen J, Shao P, Chen Y, Wang L, Lv X, Yang W, Jia Y, Jiang Z, Zhu B, Qu L. Genomic scan revealed KIT gene underlying white/gray plumage color in Chinese domestic geese. Anim Genet, 2021, 52(3): 356-360. pmid: 33644907
[24]	Wen JH, Yu JC, Zhang L, Li HY, Wang HE, Gu HC, Zhao XR, Zhang XY, Ren XF, Wang G, Chen AQ, Qu LJ. Genomic analysis reveals candidate genes underlying sex-linked eyelid coloboma, feather color traits, and climatic adaptation in Huoyan geese. Animals (Basel), 2023, 13(23): 3608. pmid: 38066959
[25]	Nannan M, Wenjun W, Ran Z, Yongsheng S, Rongyan Z, Hui C, Sumin Z, Hui X. Population genomics reveals that a missense mutation in EDNRB2 contributes to white plumage color in pigeons. Poult Sci, 2024, 103(1): 103225. pmid: 38035860
[26]	Maclary ET, Wauer R, Phillips B, Brown A, Boer EF, Samani AM, Shapiro MD. An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon. PLoS Genet, 2023, 19(10): e1010880. pmid: 37862332
[27]	Domyan ET, Guernsey MW, Kronenberg Z, Krishnan S, Boissy RE, Vickrey AI, Rodgers C, Cassidy P, Leachman SA, Fondon JW, Yandell M, Shapiro MD. Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Curr Biol, 2014, 24(4): 459-464. pmid: 24508169
[28]	冯春刚, 胡晓湘, 赵要风, 李宁. 全基因组选择及其在动物育种中的应用. 中国家禽, 2008, 30(22): 5-8.

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引物名称	登录号	序列(5′→3′)	目标染色体	产物长度(bp)	退火温度(℃)
Yuse-3SNP	NC_088613.1	F: AAACGGAGCCTACAATAAAGAGCA R: TGTGGTGTGGGCATGAAAGAAA	4	1,022	57
Yuse-2InDel	NC_088613.1	F: GAAGATGGGAGAAGGAAAGAGCAC R: AGTCTTTAGGGTGTCTGCATGG	4	1,023	57

位点类别	碱基突变	目标位点	基因区域	氨基酸变化	突变类型
羽色相关的SNP位点	G→A	Chr4 g.20149025	基因1号内含子	非编码区	无
	A→G	Chr4 g.20148382	基因2号外显子	缬氨酸	同义突变
	T→C	Chr4 g.20148997	基因1号内含子	非编码区	无
羽色相关的InDel位点	A→AATCAGCTCTACCTAACTCA	Chr4 g.20166449	基因间区	非编码区	无
羽色相关的InDel位点	A→AA	Chr4 g.20166666	基因间区	非编码区	无

目标位点	品种	样本数	基因型(个体数/频率)
g.20149025 G>A			GG	GA	AA
	天翔鸽(白羽)	30	30(1.000)	0(0.000)	0(0.000)
	塔里木鸽(灰羽)	12	0(0.000)	1(0.083)	11(0.917)
	广东黑鸽(黑羽)	30	0(0.000)	14(0.467)	16(0.533)
g.20148382 A>G			AA	AG	GG
	天翔鸽(白羽)	30	30(1.000)	0(0.000)	0(0.000)
	塔里木鸽(灰羽)	12	0(0.000)	1(0.083)	11(0.917)
	广东黑鸽(黑羽)	30	0(0.000)	14(0.467)	16(0.533)
g.20148997 T>C			TT	TC	CC
	天翔鸽(白羽)	30	30(1.000)	0(0.000)	0(0.000)
	塔里木鸽(灰羽)	12	0(0.000)	1(0.083)	11(0.917)
	广东黑鸽(黑羽)	30	0(0.000)	14(0.467)	16(0.533)

目标位点	品种	样本数	基因型(个体数/频率)
目标位点	品种	样本数	DD	ID	II
g.20166449 A>AATCAGCTCTACCTAACTCA	天翔鸽(白羽)	30	30(1.000)	0(0.000)	0(0.000)
	塔里木鸽(灰羽)	12	0(0.000)	4(0.333)	8(0.667)
	广东黑鸽(黑羽)	39	3(0.077)	9(0.231)	27(0.692)
g.20166666 A>AA	天翔鸽(白羽)	30	30(1.000)	0(0.000)	0(0.000)
	塔里木鸽(灰羽)	12	0(0.000)	4(0.333)	8(0.667)
	广东黑鸽(黑羽)	39	3(0.077)	9(0.231)	27(0.692)

广东黑鸽群体遗传结构解析及基于全基因组关联分析的黑羽性状相关变异位点验证

Population genetic structure analysis of Guangdong Black pigeon and validation of black plumage trait-associated loci based on genome-wide association study

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