永登七山羊全基因组选择信号检测分析

doi:10.11843/j.issn.0366-6964.2023.11.014

摘要/Abstract

摘要： 旨在检测永登七山羊群体基因组选择信号,挖掘永登七山羊有价值的种质特性基因。本研究以4个绵羊群体(永登七山羊、岷县黑裘皮羊、兰州大尾羊和滩羊)共40个个体为研究对象,利用简化基因组测序(specific-locus amplified fragment sequencing,SLAF-seq)技术检测全基因组范围内的单核苷酸多态性位点(SNPs)。基于SNPs数据集,通过elgensoft软件进行主成分分析;运用Treemix软件分析基因流事件;利用群体遗传分化指数(Fst)和核苷酸多样性比值(π ratio)进行全基因组选择性清除分析,取top 5% Fst和π ratio的交集以确定基因组受选择区域,并对候选基因进行GO和KEGG富集分析。结果共得到1 658 596个群体SNPs;主成分分析(PCA)发现永登七山羊能够独立分群,基因流表明永登七山羊和兰州大尾羊存在较弱的基因交流。以永登七山羊为试验群体,岷县黑裘皮羊、兰州大尾羊和滩羊为参考群体进行选择清除分析,3个比较组的受选择区域分别检测出424、294、301个候选基因;GO和KEGG分析结果表明,候选基因分别显著富集在65、79、41个GO条目及15、22、10条KEGG通路上(P＜0.05)。此外,将岷县黑裘皮羊、兰州大尾羊和滩羊3个群体的数据合并为一个数据集与永登七山羊进行比较,共筛选到466个候选基因,显著富集到124个GO条目及7条KEGG通路(P＜0.05)。从中筛选到永登七山羊重要经济性状相关的功能基因BMP2、GRM1和ALDH1A1。研究结果表明,在永登七山羊全基因组范围内进行选择信号检测,鉴定到与生长发育、脂尾进化相关的候选基因,为永登七山羊的分子遗传标记挖掘提供参考。

关键词: 永登七山羊, 简化基因组测序, 基因流, 选择性清除分析, 功能富集

Abstract: The aim of this study was to detect genomic selection signals in the Yongdeng Qishan sheep population and to mine valuable germplasm trait genes. A total of 40 individuals from 4 sheep populations (Yongdeng Qishan sheep, Minxian black fur sheep, Lanzhou fat-tailed sheep, Tan sheep) were used as study subjects to detect genome-wide single nucleotide polymorphism sites (SNPs) using specific-locus amplified fragment sequencing (SLAF-seq). Based on SNPs data, elgensoft software was used for principal component analysis (PCA), gene flow events were analyzed by Treemix software. Selective sweep analysis was performed using population genetic differentiation index (Fst) and nucleotide diversity ratio (π ratio) and the intersection of top 5% Fst and π ratio was taken to identify selected genomic regions. The GO and KEGG enrichment analysis of candidate genes was performed. A total of 1 658 596 population SNPs were obtained; Principal component analysis (PCA) found that Yongdeng Qishan sheep were able to independently group, gene flow showed that there was weak gene exchange between Yongdeng Qishan sheep and Lanzhou fat-tailed sheep. Yongdeng Qishan sheep were used as the experimental group, and Minxian black fur sheep, Lanzhou fat-tailed sheep and Tan sheep were used as the reference group for selection sweep analysis. The 424, 294 and 301 candidate genes were detected in the selected regions of the 3 comparison groups; GO and KEGG analyses showed that the candidate genes were significantly enriched in 65, 79 and 41 GO terms and 15, 22 and 10 KEGG pathways, respectively (P＜0.05). In addition, SNP datas from 3 populations of Minxian black fur sheep, Lanzhou fat-tailed sheep and Tan sheep were combined into one dataset for comparison with Yongdeng Qishan sheep and 466 candidate genes were significantly enriched to 124 GO terms and 7 KEGG pathways (P＜0.05).Functional genes BMP2, GRM1, and ALDH1A1 related to important economic traits were screened from Yongdeng Qishan sheep. The research shows that the selection signal detection in the whole genome of Yongdeng Qishan sheep can identify candidate genes related to growth and development and fat tail evolution, providing reference for molecular genetic marker mining of Yongdeng Qishan sheep.

Key words: Yongdeng Qishan sheep, specific-locus amplified fragment sequencing, gene flow, selective sweep analysis, functional enrichment

中图分类号:

S826.2

栗登攀, 马克岩, 韩金涛, 白雅琴, 李讨讨, 马友记. 永登七山羊全基因组选择信号检测分析[J]. 畜牧兽医学报, 2023, 54(11): 4577-4588.

LI Dengpan, MA Keyan, HAN Jintao, BAI Yaqin, LI Taotao, MA Youji. Detection and Analysis of Whole Genome Selection Signal of Yongdeng Qishan Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4577-4588.

参考文献 48

[1]	马克岩,韩金涛,白雅琴,等.基于简化基因组测序的永登七山羊遗传多样性分析[J].畜牧兽医学报,2023,54(5):1939-1950.MA K Y,HAN J T,BAI Y Q,et al.Genetic diversity analysis of Yongdeng Qishan sheep based on specific-locus amplified fragment sequencing[J].Acta Veterinaria et Zootechnica Sinica,2023,54(5):1939-1950.(in Chinese)
[2]	TONG X L,HAN M J,LU K P,et al.High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation[J].Nat Commun,2022,13(1):5619.
[3]	GONG Y,LI Y F,LIU X X,et al.A review of the pangenome:how it affects our understanding of genomic variation,selection and breeding in domestic animals?[J].J Anim Sci Biotechnol,2023,14(1):73.
[4]	GUO J Z,TAO H X,LI P F,et al.Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds[J].Sci Rep,2018,8(1):10405.
[5]	LI R N,ZHAO Y H T,LIANG B M,et al.Genome-wide signal selection analysis revealing genes potentially related to sheep-milk-production traits[J].Animals (Basel),2023,13(10):1654.
[6]	SHI H B,LI T T,SU M C,et al.Whole genome sequencing revealed genetic diversity,population structure,and selective signature of Panou Tibetan sheep[J].BMC Genomics,2023,24(1):50.
[7]	薛周舣源,宋显威,吴林慧,等.畜禽选择信号检测方法及其统计学问题[J].畜牧兽医学报,2018,49(6):1099-1107.XUE Z Y Y,SONG X W,WU L H,et al.The identification methods of selection signatures in livestock and its statistical problems[J].Acta Veterinaria et Zootechnica Sinica,2018,49(6):1099-1107.(in Chinese)
[8]	TALEBI R,GHAFFARI M R,ZEINALABEDINI M,et al.Genetic basis of muscle-related traits in sheep:a review[J].Anim Genet,2022,53(6):723-739.
[9]	PAN Z Y,LI S D,LIU Q Y,et al.Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization[J].Gigascience,2018,7(4):giy019.
[10]	LI X,YANG J,SHEN M,et al.Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits[J].Nat Commun,2020,11(1):2815.
[11]	LI Y F,GONG Y,ZHANG Z K,et al.Whole-genome sequencing reveals selection signals among Chinese,Pakistani,and Nepalese goats[J].J Genet Genomics,2023,50(5):362-365.
[12]	LI H,DURBIN R.Fast and accurate long-read alignment with burrows-wheeler transform[J].Bioinformatics,2010,26(5):589-595.
[13]	MCKENNA A,HANNA M,BANKS E,et al.The genome analysis toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J].Genome Res,2010,20(9):1297-1303.
[14]	LI H,HANDSAKER B,WYSOKER A,et al.The sequence alignment/map format and SAMtools[J].Bioinformatics, 2009,25(16): 2078-2079.
[15]	CINGOLANI P,PLATTS A,WANG L L,et al.A program for annotating and predicting the effects of single nucleotide polymorphisms,SnpEff:SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3[J].Fly (Austin),2012,6(2):80-92.
[16]	PRICE A L,PATTERSON N J,PLENGE R M,et al.Principal components analysis corrects for stratification in genome-wide association studies[J].Nat Genet,2006,38(8):904-909.
[17]	WEBER D,STEWART B S,GARZA J C,et al.An empirical genetic assessment of the severity of the northern elephant seal population bottleneck[J].Curr Biol,2000,10(20):1287-1290.
[18]	IVEY C T,HABECKER N M,BERGMANN J P,et al.Weak reproductive isolation and extensive gene flow between Mimulus glaucescens and M. guttatus in northern California[J].Evolution,2023,77(5):1245-1261.
[19]	邱小宇,黄勇富,赵永聚,等.中国6个地方绵羊品种的微卫星分析[J].中国畜牧兽医,2016,43(4):1024-1031.QIU X Y,HUANG Y F,ZHAO Y J,et al.Microsatellite analysis of six Chinese indigenous sheep breeds[J].China Animal Husbandry & Veterinary Medicine,2016,43(4):1024-1031.(in Chinese)
[20]	韩旭,刘丑生,刘刚,等.中国地方绵羊线粒体DNA D-loop区遗传多样性研究[J].中国畜牧杂志,2015,51(7):10-15.HAN X,LIU C S,LIU G,et al.Study on genetic diversity of D-loop region of mitochondrial DNA of domestic sheep in China[J]. Chinese Journal of Animal Science,2015,51(7):10-15.(in Chinese)
[21]	SUAREZ-GONZALEZ A,LEXER C,CRONK Q C B.Adaptive introgression:a plant perspective[J].Biol Lett,2018,14(3): 20170688.
[22]	SATOKANGAS I,NOUHAUD P,SEIFERT B,et al.Semipermeable species boundaries create opportunities for gene flow and adaptive potential[J].Mol Ecol,2023,32(15):4329-4347.
[23]	JANSSON E,FAUST E,BEKKEVOLD D,et al.Global,regional,and cryptic population structure in a high gene-flow transatlantic fish[J].PLoS One,2023,18(3):e0283351.
[24]	LI X L,YUAN L F,WANG W M,et al.Whole genome re-sequencing reveals artificial and natural selection for milk traits in east Friesian sheep[J].Front Vet Sci,2022,9:1034211.
[25]	LIU L L,MENG J,MA H Y,et al.Candidate genes for litter size in Xinjiang sheep identified by specific locus amplified fragment (SLAF) sequencing[J].Anim Biotechnol,2023,34(7):3053-3062.
[26]	CRISPIM A C,KELLY M J,GUIMARAES S E F,et al.Multi-trait GWAS and new candidate genes annotation for growth curve parameters in Brahman cattle[J].PLoS One,2015,10(10):e0139906.
[27]	KIM E S,ELBELTAGY A R,ABOUL-NAGA A M,et al.Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment[J].Heredity (Edinb),2016,116(3):255-264.
[28]	LU Z K,DU L X,LIU R Z,et al.MiR-378 and BMP-smad can influence the proliferation of sheep myoblast[J].Gene,2018, 674:143-150.
[29]	KALDS P,LUO Q,SUN K,et al.Trends towards revealing the genetic architecture of sheep tail patterning:promising genes and investigatory pathways[J].Anim Genet,2021,52(6):799-812.
[30]	SERRANITO B,CAVALAZZI M,VIDAL P,et al.Local adaptations of Mediterranean sheep and goats through an integrative approach[J].Sci Rep,2021,11(1):21363.
[31]	LU Z K,LIU J B,HAN J L,et al.Association between BMP2 functional polymorphisms and sheep tail type[J].Animals (Basel),2020,10(4):739.
[32]	ZHANG Z B,LIU Q Y,DI R,et al.Single nucleotide polymorphisms in BMP2 and BMP7 and the association with litter size in Small Tail Han sheep[J].Anim Reprod Sci,2019,204:183-192.
[33]	ZHANG L,LIU J S,ZHAO F P,et al.Genome-wide association studies for growth and meat production traits in sheep[J].PLoS One,2013,8(6):e66569.
[34]	ZHU M T,ZHANG H M,YANG H,et al.Polymorphisms and association of GRM1,GNAQ and HCRTR1 genes with seasonal reproduction and litter size in three sheep breeds[J].Reprod Domest Anim,2022,57(5):532-540.
[35]	GOSSNER A G,HOPKINS J.Transcriptome analysis of CNS immediately before and after the detection of PrPSc in SSBP/1 sheep scrapie[J].Vet Microbiol,2014,173(3-4):201-207.
[36]	聂玮,孟科,荣轩,等.绵羊GRM1基因多态性及其与肉质性状的相关性[J].浙江农业学报,2023,35(4):799-808.NIE W,MENG K,RONG X,et al.Analysis of GRM1 gene polymorphism and its correlation with meat quality traits in sheep[J].Acta Agriculturae Zhejiangensis,2023,35(4):799-808.(in Chinese)
[37]	WANG X Y,FANG C,HE H Y,et al.Identification of key genes in sheep fat tail evolution based on RNA-seq[J].Gene,2021,781: 145492.
[38]	康丹菊.绵羊脂肪沉积关键基因的筛选及ALDH1As在脂肪细胞分化中的调控研究[D].杨凌:西北农林科技大学,2018.KANG D J.Identification of key genes related to adipose deposition in sheep and regulatory study of ALDH1As in adipocyte differentiation[D].Yangling:Northwest A&F University,2018.(in Chinese)
[39]	LIU S Q,LIU Z Y,WANG P,et al.Estrogen-mediated oar-miR-485-5p targets PPP1R13B to regulate myoblast proliferation in sheep[J].Int J Biol Macromol,2023,236:123987.
[40]	DUAN Z,JI X,ZHU Y X,et al.Effects of sheep bone collagen peptide on liver lipid deposition in ovariectomized rats[J].J Nutr Sci Vitaminol (Tokyo),2022,68(4):320-330.
[41]	LI Q,MILLAR R P,CLARKE I J,et al.Evidence that neurokinin b controls basal gonadotropin-releasing hormone secretion but is not critical for estrogen-positive feedback in sheep[J].Neuroendocrinology,2015,101(2):161-174.
[42]	SUN H R,MENG K,WANG Y F,et al.LncRNAs regulate the cyclic growth and development of hair follicles in Dorper sheep[J].Front Vet Sci,2023,10:118629.
[43]	WU C L,LI J Y,XU X M,et al.Effect of the FA2H Gene on cashmere fineness of Jiangnan cashmere goats based on transcriptome sequencing[J].BMC Genomics,2022,23(1):527.
[44]	HE D Q,CHEN L Y,LUO F,et al.Differentially phosphorylated proteins in the crimped and straight wool of Chinese Tan sheep[J].J Proteomics,2021,235:104115.
[45]	PLOWMAN J E,HARLAND D P,RICHENA M,et al.Wool fiber curvature is correlated with abundance of K38 and specific keratin-associated proteins[J].Proteins,2022,90(4):973-981.
[46]	MORGAN H J,BENKETAH A,OLIVERO C,et al.Hair follicle differentiation-specific keratin expression in human basal cell carcinoma[J].Clin Exp Dermatol,2020,45(4):417-425.
[47]	KOWALCZYK A,CHIKINA M,CLARK N.Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness[J].Elife,2022,11:e76911.
[48]	HUI T Y,ZHENG Y Y,YUE C,et al.Screening of cashmere fineness-related genes and their ceRNA network construction in cashmere goats[J].Sci Rep,2021,11(1):21977.