基于全基因组重测序分析豁眼鹅(五龙鹅)遗传多样性和保种效果

doi:10.11843/j.issn.0366-6964.2025.12.019

Abstract

Abstract: This study aimed to investigate the genetic diversity and inbreeding status of the Huoyan geese (Wulong geese) conservation population using whole-genome resequencing, evaluate the effectiveness of current germplasm conservation strategies, and provide actionable insights for future breeding programs. A total of 40 male Huoyan geese (Wulong geese) were randomly selected from the Shandong Provincial Conservation Farm for whole-genome resequencing. Subsequent analyses included assessments of genetic diversity, population genetic structure, and runs of homozygosity (ROH). The results showed that: a total of 40 slit-eyed geese (Wulong geese) were sequenced with an average depth of 13×, and 13 251 291 SNP loci were identified after quality control. The average polymorphism information content (PIC) of this conservation population was 0.264, the average observed heterozygosity (Ho) was 0.323, and the average expected heterozygosity (He) was 0.327, with an inbreeding coefficient (F) of 0.012. LD decay analysis showed that the maximum R² value was 0.47, with a decay distance of 162 kb. A total of 309 runs of homozygosity (ROH) were detected in the Huoyan Goose (Wulong Goose) conservation population. The inbreeding coefficient (F_ROH) calculated based on ROH was 0.009, indicating a low level of inbreeding within the population. The results of the IBS distance matrix and G matrix showed simi-lar trends, with only a small proportion of individuals exhibiting close kinship. Principal component analysis (PCA) and neighbor-joining (NJ) clustering analysis further confirmed that the conservation population was generally in a dispersed state. Overall, the genetic diversity of the Huoyan goose (Wulong goose) conservation population surveyed in Laiyang was favorable, with a low level of inbreeding, indicating effective conservation efforts.

Key words: Huoyan goose, conservation efficacy, whole-genome resequencing, genetic diversity, inbreeding

CLC Number:

S835.2

TENG Xingyi, WANG Baowei, ZHANG Ming'ai, KONG Min, SHU Yindong, WANG Fenghao, JIANG Yajing, LU Xiu, HUAI Zhifang, ZANG Yuting, HUANG Luyu, FAN Wenlei. The Evaluation of Conservation Efficacy and Population Genetic Diversity in Huoyan Geese (Wulong Geese) Based on Whole-Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(12): 6159-6166.

References

[1] 中国畜牧业信息网.国家级畜禽遗传资源保护名录中华人民共和国农业部公告第662号[J].吉林畜牧兽医，2019,40(1):55.
China Livestock Information Network.National livestock and poultry genetic resources protection list.Announcement No.662 of the Ministry of Agriculture of the People's Republic of China[J].Jilin Animal Husbandry and Veterinary Medicine,2019,40(1):55.(in Chinese)
[2] 杨婷，郑浩，连林生.畜禽保种理论与方法研究进展[J].家畜生态学报，2007,(4)：109-112.
YANG T, ZHENG H, LIAN L S. Recent advances on theories motheds of conservation of livestock and poultry [J].Journal of Domestic Animal Ecology, 2007，(4): 109-112. (in Chinese)
[3] 肖煜.五龙鹅豁眼性状转录组分析及FREM1基因突变位点相关性初步探究[D].聊城：聊城大学，2024.
XIAO Y. Transcriptome analysis of Huoyan trait in Wulong goose and preliminary exploration of the correlation of mutation sites in the FREM1 [D].Liaocheng: Liaocheng University, 2024. (in Chinese)
[4] 邬欣桐.云南灰鹅与其他6个家鹅群体遗传多样性比较分析[D].昆明：云南农业大学，2023.
WU X T. Comparative analysis of genetic diversity between Yunnan gray goose and other six domestic goose populations [D].Kunming: Yunnan Agricultural University, 2023. (in Chinese)
[5] 刘一江.鸡微卫星DNA指纹图谱初步构建与种质资源纯度鉴定的研究[D].长春：吉林农业大学，2024.
LIU Y J. Preliminary construction of chicken microsatellite DNA fingerprinting and purity identification of germplasm resources [D].Changchun: Jilin Agricultural University, 2024. (in Chinese)
[6] 赵桂群.鸡SSR-DNA指纹图谱初步构建与种质资源亲缘关系鉴定的研究[D].长春：吉林农业大学，2024.
ZHAO G Q. Study of preliminary construction of SSR-DNA fingerprinting and identification of genetic relationship in germplasm resources of chickens [D].Changchun: Jilin Agricultural University, 2024. (in Chinese)
[7] ŞAHIN Z, MERCAN L. Analysis of genetic variations in Turkish domestic goose populations and Chinese×Embden crosses using microsatellite markers[J].GENETIKA, 2023, 55: 707-718.
[8] ALSHAWI A, ESSA A, AL-BAYATTI S, et al. Genome analysis reveals genetic admixture and signature of selection for productivity and environmental traits in Iraqi Cattle[J].Front Genet, 2019, 10: 609.
[9] 刘冉冉，赵桂苹，文杰.鸡基因组育种和保种用SNP芯片研发及应用[J].中国家禽，2018，40(15)：1-6.
LIU R R, ZHAO G P, WEN J. Development of genome-wide SNP genotyping arrays for chicken breeding and conservation [J]. China Poultry, 2018, 40(15): 1-6. (in Chinese)
[10] TOSSER-KLOPP G, BARDOU P, BOUCHEZ O, et al. Design and characterization of a 52K SNP chip for goats[J].PLoS One, 2014, 9(1): 1-8.
[11] KON T, PEI L, ICHIKAWA R, et al. Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation[J].Sci Rep, 2021, 11(1): 11235.
[12] YU S, LIU Z, LI M, et al. Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection[J].GigaSci, 2023, 12: giad016.
[13] SHI H, LI T, SU M, et al. Whole genome sequencing revealed genetic diversity, population structure, and selective signature of Panou Tibetan sheep[J]. BMC Genomics, 2023, 24(1): 50.
[14] TAO L, HE X Y, JIANG Y T, et al. Combined approaches to reveal genes associated with litter size in Yunshang black goats[J].Anim Genet, 2020, 51(6): 924-934.
[15] 万伟粲，张旭，黄璇，等.基于全基因组重测序分析酃县白鹅保种效果[J].中国畜牧兽医，2024，51(11)：4890-4898.
WAN W C, ZHANG X, HUANG X, et al. Assessment of conservation effects of Lingxian White goose based on whole genome resequencing [J].China Animal Husbandry & Veterinary Medicine, 2024, 51(11): 4890-4898. (in Chinese)
[16] 徐扩卫，李卓辉，冷堂健，等.基于全基因组重测序SNP分析宁蒗高原鸡保种群的群体遗传多样性和群体遗传结构[J].畜牧兽医学报，2024，55(12)：5498-5510.
XU K W, LI Z H, LENG T J, et al. Analysis of population genetic diversity and population genetic structure of conservation population in ninglang plateau chickens based on whole-genome resequencing SNP [J].Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5498-5510. (in Chinese)
[17] 中国畜牧业协会2024年工作总结[J].畜牧产业，2025,(3)：4-9.
Work Summary of China Animal Agriculture Association in 2024 [J].Animal Agriculture, 2025(3): 4-9. (in Chinese)
[18] 朱明霞，刘静静，张淑二，等.山东省水禽种业发展成效、问题分析与前景[J].中国禽业导刊，2021，38(5)：12-15.
ZHU M X, LIU J J, ZHANG S E, et al. Achievements, problem analysis and prospects of the development of waterfowl seed industry in Shandong province [J].Guide to Chinese Poultry, 2021, 38(5): 12-15. (in Chinese)
[19] 邹剑敏，李慧芳，陈宽维，等.我国家鸭品种资源遗传多样性保护等级分析[J].畜牧兽医学报，2011，42(1)：25-32.
ZOU J M, LI H F, CHEN K W, et al. Conservation priorities of chinese indigenous duck breeds [J].Acta Veterinaria et Zootechnica Sinica, 2011, 42(1): 25-32. (in Chinese)
[20] 陈皖强.部分珍稀濒危地方鸡品种遗传多样性分析与评估[D].北京：中国农业科学院，2024.
CHEN W Q. Analysis and evaluation of genetic diversity of some rare and endangered local chicken breeds [D].Beijing: Chinese Academy of Agricultural Sciences, 2024. (in Chinese)
[21] 刘珍妮，成笛，孔智伟，等.基于全基因组重测序对大余鸭的遗传进化分析[J].中国畜牧杂志，2024，60(11)：179-184.
LIU Z N, CHENG D, KONG Z W, et al. Genetic and evolutionary analysis of Dayu Ducks based on whole-genome resequencing [J].Chinese Journal of Animal Science, 2024, 60(11): 179-184. (in Chinese)
[22] 郭徵力，赵中龙，杨红，等.织金白鹅微卫星标记遗传多样性及其与体尺指标的关联分析[J].农业生物技术学报，2023，31(11)：2341-2357.
GUO Z L, ZHAO Z L, YANG H, et al. Genetic diversity of microsatellite markers in Zhijin White geese (Anser cygnoides orientalis) and its association analysis with body size indexes [J].Journal of Agricultural Biotechnology, 2023, 31(11): 2341-2357. (in Chinese)
[23] 黄红艳，张力允，黄智荣，等.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.
HUANG H Y, ZHANG L Y, HUANG Z R, et al. 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. (in Chinese)
[24] 万伟粲，何旭，刘洋，等.基于全基因组重测序分析道州灰鹅保种效果[J].畜牧兽医学报，2025，56(2)：633-642.
WAN W C, HE X, LIU Y, et al. Evaluation of Daozhou Gray goose conservation based on whole genome resequencing analysis [J].Acta Veterinaria et Zootechnica Sinica, 2025, 56(2): 633-642. (in Chinese)
[25] 张夕霏，葛华梁，赵然，等.基于全基因组重测序分析坝上长尾鸡遗传多样性与保种效果[J].中国畜牧杂志，2024，60(11)：120-126.
ZHANG X F, GE H L, ZHAO R, et al. Analysis of the genetic diversity and conservation effect of Bashang Long-tailed chickens based on whole-genome resequencing [J].Chinese Journal of Animal Science, 2024, 60(11): 120-126. (in Chinese)
[26] 王宏宁.地方鹅生长速度性状全基因组选择信号和关联分析研究[D].扬州：扬州大学，2024.
WANG H N. Genome-wide selection signals and association analysis of growth rate traits in local geese [D].Yangzhou: Yangzhou University, 2024. (in Chinese)
[27] 郭其新.鸭系统演化及重要经济性状候选基因挖掘[D].扬州：扬州大学，2023.
GUO Q X. Duck phylogeny and candidate gene mining for important economically traits [D].Yangzhou: Yangzhou University, 2023. (in Chinese)
[28] 林燕.基于全基因组重测序数据的广东省地方鹅群体遗传学研究[D].广州：仲恺农业工程学院，2023.
LIN Y. Population genetics of indigenous geese in Guangdong province based on whole-genome resequencing data [D].Guangzhou: Zhongkai University of Agriculture and Engineering, 2023. (in Chinese)

The Evaluation of Conservation Efficacy and Population Genetic Diversity in Huoyan Geese (Wulong Geese) Based on Whole-Genome Resequencing

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