全基因组数据揭示丰城麻鸭的种质资源特性与遗传多样性特征

doi:10.3864/j.issn.0578-1752.2026.11.015

摘要/Abstract

摘要：

【目的】探讨丰城麻鸭（Fengcheng duck，FCD）与中国不同地域地方鸭之间的系统发育关系，解析FCD及其他地方鸭群体的遗传多样性和遗传结构，为中国地方鸭资源的鉴定与保护提供理论基础。【方法】采集35只丰城麻鸭的全血样本进行12×全基因组重测序，整合来自中国不同地区的12个品种共420只个体的基因组数据，涵盖13个品种共455只个体。以高质量的吉安红毛鸭基因组为参考，使用GATK软件检测基因组单核苷酸多态性（single nucleotide polymorphisms， SNP），通过SnpEff软件对所有变异进行注释。基于常染色体SNP，构建系统进化树，进行PCA聚类和Admixture分析评估地方鸭的群体结构，同时通过统计常见SNPs、期望杂合度、实际杂合度、近交系数、种群内遗传距离和纯合片段等6个参数评估种群的遗传多样性，并通过群体分化指数（Fst）量化种群间的分化程度。【结果】FCD群体中共检测到8 656 794个SNP，平均每132个碱基存在一个变异。结合其他地方鸭的基因组数据，共检测到8 889 170个SNP，主要富集在基因间区（45.50%），其次是内含子区（32.82%）、基因上游区（9.74%）、基因下游区（9.27%）和外显子区（1.67%）。在蛋白质编码基因中，鉴定出54 150个错义变异、117 021个同义变异、74 667个3'UTR变异、73个起始密码子变异、1 162个终止缺失变异、210个起始缺失变异及2 346个终止获得变异。系统进化树、PCA和Admixture分析结果显示，各品种单独聚类，肉用型、兼用型和蛋用型鸭类群之间存在显著分化，不同品种间的亲缘关系更多基于经济用途而非地理距离。FCD与蛋鸭类群聚类，尤其与攸县麻鸭亲缘关系最近。不同鸭品种间部分个体存在遗传混杂现象，北京鸭和金定鸭具有较高的近交系数、较少的常见SNP数量、低杂合率和较长的纯合片段，说明强人工选择导致其遗传多样性降低，而FCD的常见SNP数量和杂合度最高，显示出丰富的遗传多样性。【结论】通过全基因组SNP标记，系统解析了中国地方鸭及丰城麻鸭的群体遗传结构和多样性特征，为中国地方鸭的独立分类和保护利用提供了重要的数据支持。

关键词: 丰城麻鸭, 中国地方鸭, 全基因组SNPs, 群体结构, 遗传多样性

Abstract:

【Objective】 This study aims to investigate the phylogenetic relationships between Fengcheng duck (FCD) and Chinese indigenous duck breeds, analyze the genetic diversity and genetic structure of FCD and other duck breeds, so as to provide a theoretical foundation for the identification and conservation of Chinese indigenous duck resources. 【Method】 Whole-genome resequencing at 12× coverage was performed on blood samples from 35 FCD individuals. Genome data from 420 individuals of 12 breeds from different regions in China were integrated, totaling 455 individuals across 13 breeds. Using a high-quality Ji'an Red duck genome as a reference, genome single nucleotide polymorphisms (SNPs) were detected using GATK software, and all variants were annotated using SnpEff software. Based on autosomal SNPs, a phylogenetic tree was constructed, and PCA clustering and Admixture analysis were performed to assess the population structure of indigenous ducks. Six parameters, were used to evaluate population genetic diversity, including common SNPs, expected heterozygosity, observed heterozygosity, inbreeding coefficient, population genetic distance, and runs of homozygosity, and the fixation index (Fst) was employed to quantify the degree of differentiation between populations.【Result】A total of 8 656 794 SNPs were detected in the FCD population, with an average of one variant per 132 base pairs. Combined with the genomic data of other local duck breeds, a total of 8 889 170 SNPs were detected, which were mainly enriched in intergenic regions (45.50%), followed by intronic regions (32.82%), upstream regions (9.74%), downstream regions (9.27%), and exonic regions (1.67%). In protein-coding genes, 54 150 missense mutations, 117 021 synonymous mutations, 74 667 3'UTR mutations, 73 start codon mutations, 1 162 stop-loss mutations, 210 start-loss mutations, and 2 346 stop-gain mutations were identified. The results of the phylogenetic tree, PCA, and Admixture analyses showed that each breed clustered independently, with significant differentiation among meat-type, dual-purpose, and egg-type duck groups. The relationships between different breeds were more based on economic use rather than geographical distance. FCD clustered with egg-type duck groups, particularly showing the closest relationship with Youxian duck. Genetic admixture was observed among some individuals of different duck breeds. Beijing duck and Jinding duck had higher inbreeding coefficients, fewer common SNPs, lower heterozygosity, and longer runs of homozygosity, indicating reduced genetic diversity due to strong artificial selection, whereas FCD exhibited the highest number of common SNPs and heterozygosity, indicating rich genetic diversity. 【Conclusion】 Using whole-genome SNP markers, this study systematically analyzed the genetic structure and diversity characteristics of Chinese indigenous ducks and Fengcheng ducks, providing important data support for the independent classification and conservation of Chinese indigenous duck resources.

Key words: Fengcheng duck, Chinese local duck, whole-genome SNPs, population structure, genetic diversity

缪俊杰, 谢平华, 廖小华, 毛辉荣, 谢冲冲, 周婧, 谭红丽, 吴利平, 王雅楠, 欧阳婧, 晏学明, 陈浩. 全基因组数据揭示丰城麻鸭的种质资源特性与遗传多样性特征[J]. 中国农业科学, 2026, 59(11): 2513-2525.

MIAO JunJie, XIE PingHua, LIAO XiaoHua, MAO HuiRong, XIE ChongChong, ZHOU Jing, TAN HongLi, WU LiPing, WANG YaNan, OUYANG Jing, YAN XueMing, CHEN Hao. The Whole Genome Data Revealed the Characteristics of Germplasm Resource and Genetic Diversity of Fengcheng Ducks[J]. Scientia Agricultura Sinica, 2026, 59(11): 2513-2525.

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品种 Breed	品种代号 Breed code	样本量 Sample size	原产地 Origin region	地理气候 Geographical climate	经济类型 Economic type
巢湖麻鸭Chaohu duck	CHP	35	安徽巢湖Chaohu, Anhui	平原湿地Plain wetland	兼用型Dual-purpose
大余麻鸭Dayu duck	DYP	35	江西大余Dayu, Jiangxi	山地丘陵Mountainous hilly	兼用型Dual-purpose
丰城麻鸭Fengcheng duck	FCD	35	江西丰城Fengcheng, Jiangxi	平原湿地Plain wetland	蛋用型Egg-type
金定鸭Jinding duck	JDD	35	福建漳州Zhangzhou, Fujian	海湾滩涂Bay tidal flat	蛋用型Egg-type
吉安红毛鸭Ji'an Red-feather duck	JRD	35	江西吉安Ji'an, Jiangxi	山地丘陵Mountainous hilly	兼用型Dual-purpose
缙云麻鸭Jinyun duck	JYP	35	浙江缙云Jinyun, Zhejiang	山地丘陵Mountainous hilly	兼用型Dual-purpose
龙胜翠鸭Longsheng duck	LSD	35	广西龙胜Longsheng, Guangxi	山地丘陵Mountainous hilly	兼用型Dual-purpose
麻旺鸭Mawang duck	MWD	35	湖北鹤峰Hefeng, Hubei	山地丘陵Mountainous hilly	蛋用型Egg-type
北京鸭Peking duck	PKD	35	中国北京Beijing, China	平原Plain	肉用型Meat-type
山麻鸭Shanma duck	SPD	35	福建龙岩Longyan, Fujian	山地丘陵Mountainous hilly	蛋用型Egg-type
三穗鸭Sansui duck	SSD	35	贵州三穗Sansui, Guizhou	山地丘陵Mountainous hilly	蛋用型Egg-type
绍兴麻鸭Shaoxing duck	SXP	35	浙江绍兴Shaoxing, Zhejiang	山地丘陵Mountainous hilly	蛋用型Egg-type
攸县麻鸭Youxian duck	YXP	35	湖南攸县Youxian, Hunan	平原湿地Plain wetland	蛋用型Egg-type
总计 Total		455

品种代号 Breed code	Csnp	Pn	He	Ho	F	DST	ROH
CHP	4215869	0.903	0.283	0.271	0.16±0.04	0.238±0.010	5.90±2.43
DYP	4271257	0.961	0.292	0.28	0.13±0.04	0.246±0.007	4.64±1.24
FCD	4572552	0.985	0.312	0.307	0.09±0.10	0.259±0.006	2.19±0.94
JDD	3994489	0.844	0.263	0.249	0.25±0.03	0.221±0.008	12.17±2.81
JRD	4270744	0.911	0.284	0.27	0.16±0.04	0.239±0.008	8.89±3.07
JYP	4418259	0.953	0.298	0.282	0.15±0.04	0.252±0.012	4.92±2.92
LSD	4092656	0.903	0.276	0.261	0.21±0.04	0.233±0.013	10.89±3.66
MWD	4469107	0.966	0.303	0.285	0.13±0.03	0.257±0.010	3.77±2.30
PKD	3482916	0.821	0.241	0.141	0.57±0.05	0.230±0.004	10.67±3.06
SPD	4306058	0.93	0.289	0.273	0.17±0.04	0.244±0.013	6.86±2.49
SSD	4486689	0.964	0.303	0.291	0.12±0.05	0.254±0.013	4.52±3.49
SXP	4346655	0.949	0.294	0.278	0.15±0.02	0.249±0.010	3.70±1.44
YXP	4494220	0.973	0.305	0.289	0.13±0.06	0.258±0.007	4.55±2.87
Total	55421471

品种代号Breed code	产地Origin region	经济类型Economic type	Fst值Fst value
YXP	湖南攸县Youxian, Hunan	蛋用型Egg-type	0.021
MWD	湖北鹤峰Hefeng, Hubei	蛋用型Egg-type	0.024
JYP	浙江缙云Jinyun, Zhejiang	兼用型Dual-purpose	0.030
SSD	贵州三穗Sansui, Guizhou	蛋用型Egg-type	0.032
SPD	福建龙岩Longyan, Fujian	蛋用型Egg-type	0.042
SXP	浙江绍兴Shaoxing, Zhejiang	蛋用型Egg-type	0.042
DYP	江西大余Dayu, Jiangxi	兼用型Dual-purpose	0.054
JRD	江西吉安Ji'an, Jiangxi	兼用型Dual-purpose	0.062
JDD	福建漳州Zhangzhou, Fujian	蛋用型Egg-type	0.067
CHP	安徽巢湖Chaohu, Anhui	兼用型Dual-purpose	0.070
LSD	广西龙胜Longsheng, Guangxi	兼用型Dual-purpose	0.073
PKD	中国北京Beijing, China	肉用型Meat-type	0.102