Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (11): 2513-2525.doi: 10.3864/j.issn.0578-1752.2026.11.015

• ANIMAL SCIENCE·VETERINARY SCIENCE • Previous Articles     Next Articles

The Whole Genome Data Revealed the Characteristics of Germplasm Resource and Genetic Diversity of Fengcheng Ducks

MIAO JunJie1(), XIE PingHua2, LIAO XiaoHua3, MAO HuiRong4, XIE ChongChong2, ZHOU Jing1, TAN HongLi1, WU LiPing1, WANG YaNan1, OUYANG Jing1, YAN XueMing1, CHEN Hao1()   

  1. 1 College of Life Sciences, Jiangxi Normal University of Science and Technology, Nanchang 330013
    2 Fengcheng Feihuang Poultry Co., LTD, Fengcheng 331100, Jiangxi
    3 Fengcheng Bureau of Agriculture and Rural Affairs, Fengcheng 331100, Jiangxi
    4 Jiangxi Agricultural University, Nanchang 330045
  • Received:2024-11-29 Accepted:2026-04-17 Online:2026-06-01 Published:2026-06-03
  • Contact: CHEN Hao

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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

Fig. 1

Fengcheng duck"

Table 1

Sample origin"

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

Fig. 2

Density distribution of SNPs on chromosomes in 455 Chinese local ducks A: Density distribution of SNPS on chromosomes of 13 Chinese local duck species, with colors from blue to red indicating SNP density from low to high; B: The proportion of variation types of 13 Chinese local ducks, and the size of color block indicates the proportion of each type to the total variation"

Fig. 3

Contiguous evolutionary trees of 13 Chinese local duck species constructed based on IBS distances"

Fig. 4

Principal component analysis of autosomal SNPs in the genomes of 13 Chinese local ducks"

Fig. 5

Assessment of Admixture population structure of local ducks in China at different values of K"

Table 2

Nucleotide and genetic diversity parameters of local ducks in China"

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

Fig. 6

Genetic diversity of 13 Chinese local duck species A: The inbreeding number F of each breed, where a larger F represents more frequent inbreeding within the population; B: The intra-population genetic distance DST of each breed, where a smaller DST represents the closer relatedness of individuals within the population; C: Froh/Ho levels of each breed, with greater Froh/Ho indicating greater genetic diversity of the population; D: The distribution of ROH of homozygous fragments in each breed, with higher ROH and longer ROH indicating lower genetic diversity"

Table 3

Genetic differentiation indices between Fengcheng Duck and other local duck breeds"

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

Fig. 7

Analysis of genetic differentiation (Fst) among Chinese local duck populations under different classification criteria A: Comparisons of Fst among groups classified by economic type, including Egg-type, Meat-type, and Dual-purpose groups. B: Comparisons of Fst among groups classified by geographical region, including Central-North, East, and South-west groups Circles represent different economic or geographical groups, values on the connecting lines indicate the mean pairwise Fst between groups, and the central Mean Fst represents the overall average genetic differentiation under each classification criterion. Breed abbreviations included in each group are provided in the legend below the figure"

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