1 College of Animal Science and Technology/Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan 528225, China; 2 Jining City Animal and Veterinary Development Center, Jining 272002, China; 3 Shandong Jinxin Landes Goose Ltd. Company, Jining 272200, China; 4 Animal Genetic Breeding and Reproduction Key Laboratory of Sichuan Province/Sichuan Animal Science Academy, Chengdu 610066, China
Abstract：Since its introduction to China for more than two decades, the Landes goose (Anser anser domesticus) has formed adapted populations in several regions of the country. This study conducted whole-genome sequencing for 30 individual Jining Landes goose and downloaded the genomic data for 46 samples representing Jiangxi and French Landes goose, along with swan goose (Anser cygnoides) and grey goose (Anser anser), from the NCBI database, and then proceeded to analyze the genetic structure, runs of homozygosity (ROH), and inbreeding coefficients based on the mitochondrial genome and the whole genome information. The objective of this study was to ascertain the genetic structure and diversity of various populations of Landes geese, with the aim of providing theoretical reference for their conservation, development, and utilization in China. The results showed that the Landes goose populations in Jining and Jiangxi exhibited a conspicuous genetic affinity with the French Landes goose. However, these populations evolved to possess a more distinct population structure over the course of their long-term utilization in China. Furthermore, a degree of differentiation emerged between the 2 Landes goose populations in Jining and Jiangxi. The 3 Landes goose populations were observed to exhibit high genetic diversity. However, a comparison of the genetic diversity of the Jining Landes goose population with those of the Jiangxi and French Landes goose populations revealed that the former was lower. These findings indicated that the Jining Landes goose population experienced a greater degree of genetic diversity compared to the Jiangxi and French populations. In regard to the genetic structure, the Jining Landes goose sustained its distinct lineage, initially developing 2 relatively autonomous subgroups. A subset of this group undergone a gradual differentiation from the Jiangxi and French Landes goose groups. The Jining Landes goose group exhibited higher numbers and lengths of ROH compared to the Jiangxi and French groups. This finding suggested that artificial selection and inbreeding played a more significant role in the evolution of the Jining Landes goose group. The degree of inbreeding in the Jining Landes goose group was higher than that of the Jiangxi and French Landes goose groups which indicated that artificial selection and inbreeding played a more significant role in the Jining Landes goose group. The inbreeding coefficient of the Jining Landes goose group was found to be higher than that of the other 2 groups, however, the overall inbreeding level was found to be similar to that of other local goose breeds in China. The results of this study provide a theoretical basis for the conservation and utilization of the Landes goose in China.
[1] 高幸福, 薛垂喜, 赵廷民,等. 2024. 鱼台县特色养殖朗德鹅产业发展报告[J]. 家禽科学, 46(10): 5-9, 121. (Gao X F, Xue C X, Zhao T M, et al. 2024. Development report on the characteristic breeding of Landes goose in Yutai county[J]. China Poultry Science, 46(10): 5-9, 121.) [2] 郝家胜, 周开亚. 2000. 中国鹅5个品种遗传多样性的随机扩增多态dna分析[J]. 南京农业大学学报, 23(01): 58-62. (Hao J S, Zhou K Y.2000. RAPD analysis of genetic diversity in five breeds of domestic Chinese goose[J]. Journal of Nanjing Agricultural University, 23(01): 58-62.) [3] 何丹林, 李伟民, 方梅霞, 等. 2009. 广东省家鹅mtDNA多样性及系统进化分析[J]. 广东农业科学, (08): 177-180. (He D L, Li W M, Fang M X, et al. 2009. mtDNA diversity and phylogenetic analysisof Guangdong domestic gooses[J]. Guangdong Agricultural Sciences, (08): 177-180.) [4] 万伟粲, 何旭, 刘洋, 等. 2025. 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, 56(02): 633-642. (Wang W C, He X, Liu Y, et al.2025. Evaluation of Daozhou gray goose conservation based on whole genome resequencing analysis[J]. Acta Veterinaria et Zootechnica Sinica, 56(02): 633-642.) [5] 张岩, 魏稚彤, 虎业浩, 等. 2024. 基于全基因组重测序评估郏县红牛保种群遗传多样性与群体结构[J]. 中国畜牧兽医, 51(07): 2933-2942. (Zhang Y, Wei Z T, Hu Y H, et al.2024. Genetic diversity and population structure analysis of Jiaxian red cattle based on whole genome sequencing[J]. China Animal Husbandry & Veterinary Medicine, 51(07): 2933-2942.) [6] Alexander D H, Novembre J, Lange K.2009. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome Research, 19(9): 1655-1664. [7] Biscarini F, Nicolazzi E L, Stella A, et al.2015. Challenges and opportunities in genetic improvement of local livestock breeds[J]. Frontiers in Genetics, 6: 33. [8] Bosse M, Megens H J, Madsen O, et al.2015. Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations[J]. Genome Research, 25(7): 970-981. [9] Cardoso D F, Fernandes Junior G A, Scalez D C B, et al.2020. Uncovering sub-structure and genomic profiles in across-countries subpopulations of angus cattle[J]. Scientific Reports, 10(1): 8770. [10] Ceballos F C, Joshi P K, Clark D W, et al.2018. Runs of homozygosity: Windows into population history and trait architecture[J]. Nature Reviews Genetics, 19(4): 220-234. [11] Chen L, Cao Y, Li G, et al.2023. Population structure and selection signatures of domestication in geese[J]. Biology (Basel), 12(4): 532. [12] Chen S, Zhou Y, Chen Y, et al.2018. Fastp: An ultra-fast all-in-one fastq preprocessor[J]. Bioinformatics, 34(17): 884-890. [13] Figtree G A, Radholm K, Neal B.2019. Response by figtree et al to letter regarding article, "canagliflozin and heart failure in type 2 diabetes mellitus: Results from the canvas program (canagliflozin cardiovascular assessment study)"[J]. Circulation, 139(3): 418-419. [14] Gómez-Rubio V.2017. Ggplot2-elegant graphics for data analysis (2nd edition)[J]. Journal of Statistical Software, Book Reviews, 77(2): 1-3. [15] Gu L, Wang F, Lin Z, et al.2020. Genetic characteristics of jiaji duck by whole genome re-sequencing[J]. PLOS ONE, 15(2): e0228964. [16] Harish A, Lopes Pinto F A, Eriksson S, et al.2024. Genetic diversity and recent ancestry based on whole-genome sequencing of endangered swedish cattle breeds[J]. BMC Genomics, 25(1): 89. [17] Howrigan D P, Simonson M A, Keller M C.2011. Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms[J]. BMC Genomics, 12: 460. [18] Kumar S, Stecher G, Li M, et al.2018. Mega x: Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 35(6): 1547-1549. [19] Li H, Durbin R.2009. Fast and accurate short read alignment with burrows-wheeler transform[J]. Bioinformatics, 25(14): 1754-1760. [20] Manunza A, Noce A, Serradilla J M, et al.2016. A genome-wide perspective about the diversity and demographic history of seven spanish goat breeds[J]. Genetics, Selection, Evolution, 48(1): 52. [21] Ouyang J, Zheng S, Huang M, et al.2022. Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of chinese indigenous geese[J]. Communications Biology, 5(1): 1191. [22] Peripolli E, Munari D P, Silva M, et al.2017. Runs of homozygosity: Current knowledge and applications in livestock[J]. Animal Genetics, 48(3): 255-271. [23] Purcell S, Neale B, Todd-Brown K, et al.2007. Plink: A tool set for whole-genome association and population-based linkage analyses[J]. American Journal of Human Genetics, 81(3): 559-575. [24] Qian L, Gedong J, Qiuzhong D, et al.2019. The complete mitochondrial genome of the landes goose and its phylogenetic analyses[J]. Mitochondrial DNA Part B, 4(1): 904-905. [25] Roycroft E J, Moussalli A, Rowe K C.2020. Phylogenomics uncovers confidence and conflict in the rapid radiation of australo-papuan rodents[J]. Systematic Biology, 69(3): 431-444. [26] Rozas J, Ferrer-Mata A, Sanchez-DelBarrio J C, et al.2017. Dnasp 6: DNA sequence polymorphism analysis of large data sets[J]. Molecular Biology and Evolution, 34(12): 3299-3302. [27] Tamura K, Stecher G, Kumar S.2021. Mega 11: Molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution, 38(7): 3022-3027. [28] Thompson E A.2013. Identity by descent: Variation in meiosis, across genomes, and in populations[J]. Genetics, 194(2): 301-326. [29] van Dijk E L, Auger H, Jaszczyszyn Y, et al.2014. Ten years of next-generation sequencing technology[J]. Trends in Genetics: TIG, 30(9): 418-426. [30] Yang J, Lee S H, Goddard M E, et al.2011. Gcta: A tool for genome-wide complex trait analysis[J]. American Journal of Human Genetics, 88(1): 76-82. [31] Zhang X, Yang L, Xie Z, et al.2024. Genetic assessment and candidate genes identification for breed-specific characteristics of qingyuan partridge chicken based on runs of homozygosity[J]. BMC Genomics, 25(1): 577. [32] Zhao Q, Lin Z, Chen J, et al.2022. Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds[J]. Gigascience, 12: giad003.
