应用孟加拉国地方鸡基因组数据筛选 鸡重要性状相关基因与分子标记

摘要

鸡作为重要的经济动物,其生长、繁殖及抗病等重要性状的遗传改良,对推动养禽业高效可持续发展具有重要意义,公共数据库的建立为开展重要性状相关遗传标记的挖掘提供坚实的数据基础。利用美国国家生物技术信息中心公共数据库中的孟加拉国 3 个地方鸡品系改良前和改良后的重测序基因组数据,通过遗传多样性与选择信号分析,筛选与生长、繁殖和免疫相关的候选基因和分子标记。结果表明：改良后群体遗传多样性低于未改良群体,且改良群体呈现更慢的连锁不平衡衰减趋势,主成分分析进一步证实不同品系间存在遗传分化；通过群体分化指数与核苷酸多样性比值的联合分析,共识别出多个可能受人工选择影响的基因组区域。其中, TRAPPC8 基因在 3 个品系中均被检测到,另有 18 个基因在 2 个品系的选择信号分析中均被识别,表明这些基因可能是重要的潜在功能基因。通过基因本体和功能富集分析,共识别到与生长发育相关的通路 16 条、与生殖相关通路 4 条、与免疫功能相关通路 9 条,最终筛选得到 54 个潜在功能基因。

关键词

鸡 / 遗传多样性 / 选择信号分析 / 功能基因筛选

参考文献

[1] Macdonald K C, Edwards D N. Chickens in Africa: The importance of qasr ibrim[J]. Antiquity, 1993, 67(256): 584-590.

[2] Miao Y W, Peng M S, Wu G S, et al. Chicken domestication: An updated perspective based on mitochondrial genomes[J]. Heredity, 2013, 110(3): 277-282.

[3] Anonymous. The variation of animals and plants under domestication[J]. The British and Foreign Medico—chirurgical Review, 1868, 42(83): 143-166.

[4] Muir W M, Wong G K, Zhang Y, et al. Genome—wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds[J]. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(45): 17312-17317.

[5] Bello S F, Lawal R A, Adeola A C, et al. The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken — a review[J]. Poultry Science, 2023, 102(6). DOI:10.1016/j.psj.2023.102657.

[6] Tan X D, Liu R R, Zhao D, et al. Large—scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens[J]. Journal of Advanced Research, 2024, 55: 1-16. DOI:10.1016/j.jare.2023.02.016.

[7] Rubin C J, Zody M C, Eriksson J, et al. Whole—genome resequencing reveals loci under selection during chicken domestication[J]. Nature, 2010, 464(7288): 587-591.

[8] Das S C, Chowdhury S D, Khatun M A, et al. Poultry production profile and expected future projection in Bangladesh[J]. World's Poultry Science Journal, 2008, 64(1): 99-118.

[9] Perini F, Cendron F, Rovelli G, et al. Emerging genetic tools to investigate molecular pathways related to heat stress in chickens: a review[J]. Animals, 2020, 11(1). DOI:10.3390/ani11010046.

[10] McCarthy M I, Abecasis G R, Cardon L R, et al. Genome—wide association studies for complex traits: Consensus, uncertainty and challenges[J]. Nature Reviews. Genetics, 2008, 9(5): 356-369.

[11] Cho Y S, Go M J, Kim Y J, et al. A large—scale genome—wide association study of asian populations uncovers genetic factors influencing eight quantitative traits[J]. Nature Genetics, 2009, 41(5): 527-534.

[12] Hufford M B, Xu X, van Heerwaarden J, et al. Comparative population genomics of maize domestication and improvement[J]. Nature Genetics, 2012, 44(7): 808-811.

[13] Wang S Y, Kuang Y Y, Liang L Q, et al. Resequencing and SNP discovery of amur ide (leuciscus waleckii) provides insights into local adaptations to extreme environments[J]. Scientific Reports, 2021, 11(1). DOI:10.1038/S41598—021—84652—5.

[14] Subramanian S. The difference in the proportions of deleterious variations within and between populations influences the estimation of FST[J]. Genes, 2022, 13(2). DOI:10.3390/genes13020194.

[15] He S H, Wang Y B, Luo Y B, et al. Integrated analysis strategy of genome—wide functional gene mining reveals DKK2 gene underlying meat quality in shaziling synthesized pigs[J]. BMC Genomics, 2024, 25(1). DOI:10.1186/s12864—023—09925—x.

[16] Xin D Y, Bai Y Y, Bi Y, et al. Insertion/deletion variants within the IGF2BP2 gene identified in reported genome—wide selective sweep analysis reveal a correlation with goat litter size[J]. Journal of Zhejiang University Science B: Biomedicine & Biotechology, 2021, 22(9): 757-766.

[17] Li M Z, Tian S L, Jin L, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and tibetan wild boars[J]. Nature Genetics, 2013, 45(12): 1431-1438.

[18] Xu N Y, Zhang L Y, Chen F F, et al. Population structure, selection signal and introgression of gamecocks revealed by whole genome sequencing[J]. Journal of Animal Science and Biotechnology, 2025, 16(1). DOI:10.1186/s40104—025—01154—4.

[19] Liu C, Liu P Q, Liu S X, et al. Genetic structure, selective characterization and specific molecular identity cards of high—yielding Houdan chickens based on genome—wide SNP[J]. Poult Science. 2024, 103(12). DOI:10.1016/j.psj.2024.104325.

[20] Rabbani M A G, Vallejo—Trujillo A, Wu Z, et al. Whole genome sequencing of three native chicken varieties (common deshi, hilly and naked neck) of Bangladesh[J]. Scientific Data, 2024, 11: 1432. DOI:10.1038/s41597—024—04291—z.

[21] Faruque S, Islam M N, Bhuiyan A K F H. Ex situ improvement of indigenous chicken in Bangladesh[J]. Tropical Agricultural Research, 2015, 26(4): 596-607.

[22] Auwera G A V der, O'Connor B D. Genomics in the cloud: using docker, GATK, and WDL in terra[M]. California: O'Reilly Media, Inc., 2020.

[23] Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools[J]. Bioinformatics, 2011, 27(15): 2156-2158.

[24] Chang C C, Chow C C, Tellier L C, et al. Second—generation PLINK: Rising to the challenge of larger and richer datasets[J]. Giga Science, 2015, 4(1). DOI:10.1186/s13742—015—0047—8.

[25] Zhang C, Dong S S, Xu J Y, et al. PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files[J]. Bioinformatics (Oxford, England), 2019, 35(10): 1786-1788.

[26] Wickham H. ggplot2[M]. Cham: Springer International Publishing, 2016.

[27] Wang M S, Zhang R W, Su L Y, et al. Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication[J]. Cell Research, 2016, 26(5): 556-573.

[28] Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR[J]. Nature Protocols, 2015, 10(10): 1556-1566.

[29] Ashburner M, Ball C A, Blake J A, et al. Gene ontology: Tool for the unification of biology. The gene ontology consortium[J]. Nature Genetics, 2000, 25(1): 25-29.

[30] Kanehisa M, Goto S, Kawashima S, et al. The KEGG resource for deciphering the genome[J]. Nucleic Acids Research, 2004, 32(Database issue): 277-280.

[31] Xu S B, Hu E Q, Cai Y T, et al. Using cluster profiler to characterize multiomics data[J]. Nature Protocols, 2024, 19(11): 3292-3320.

[32] Wu S, Chen Z W, Zhou X H, et al. Analysis of genetic diversity and genetic structure of indigenous chicken populations in guizhou province based on genome—wide single nucleotide polymorphism markers[J]. Poultry Science, 2024, 103(12). DOI:10.1016/j.psj.2024.104383.

[33] Xu D, Zhu W, Wu Y H, et al. Whole—genome sequencing revealed genetic diversity, structure and patterns of selection in guizhou indigenous chickens[J]. BMC Genomics, 2023, 24(1). DOI:10.1186/s12864—023—09621—w.

[34] Chen G H, Bao W B, Shu J T, et al. Assessment of population structure and genetic diversity of 15 chinese indigenous chicken breeds using microsatellite markers[J]. Asian—Australasian Journal of Animal Sciences, 2008, 21(3): 331-339.

[35] Waples R K, Larson W A, Waples R S. Estimating contemporary effective population size in non—model species using linkage disequilibrium across thousands of loci[J]. Heredity, 2016, 117(4): 233-240.

[36] Fu W X, Dekkers J C, Lee W R, et al. Linkage disequilibrium in crossbred and pure line chickens[J]. Genetics, Selection, Evolution: GSE, 2015, 47(1). DOI:10.1186/s12711—015—0098—4.

[37] Yu S, Liang Y H. A trapper keeper for TRAPP, its structures and functions[J]. Cellular and Molecular Life Sciences: CMLS, 2012, 69(23): 3933-3944.

[38] Liu J, Xu R, Mai S J, et al. LncRNA CSMD1—1 promotes the progression of hepatocellular carcinoma by activating MYC signaling[J]. Theranostics, 2020, 10(17): 7527-7544.

[39] Chen X P, Li Y. Role of matrix metalloproteinases in skeletal muscle[J]. Cell Adhesion & Migration, 2009, 3(4): 337-341.

基金资助

国家重点研发计划项目(2021YFD1300103)

国家自然科学基金项目(32372868)

国家肉鸡产业技术体系项目(CARS-41)