基于全基因组重测序解析皮山红羊群体遗传结构及产羔数候选基因研究

doi:10.16431/j.cnki.1671-7236.2024.02.019

摘要/Abstract

摘要： 【目的】皮山红羊是分布于新疆和田地区的新发现多羔性地方绵羊品种。本研究基于全基因组重测序技术从基因组水平上了解皮山红羊的群体遗传结构及产羔性状受选择信号区域,并对候选基因进行验证。【方法】选择30只连续产2~3羔的经产皮山红羊母羊为高繁组(high fertility,HF),30只连续产单羔的经产皮山红羊母羊为低繁组(low fertility,LF),对这两个群体进行全基因组重测序。应用主成分分析(PCA)、系统进化树、群体遗传结构及全基因组扫描(Fst & θπ)等综合分析法确定候选区域,进一步筛选皮山红羊产羔性状候选基因。采用飞行质谱分型技术对候选基因进行分型验证。【结果】皮山红羊高、低繁殖组群体连锁不平衡(LD)分析衰减曲线相似,系统进化树显示两组群体分化程度不明显。PCA结果显示,两个群体明显聚成一簇,个别个体离群,其位置及相互关系符合进化树结构以及群体结构结果。设置同时达到Top 1% Z(Fst)值和θπ值的窗口为候选区域,共注释229个强选择信号,HF和LF组注释基因分别为86和143个,其中筛选到42个可能与繁殖性状相关的候选基因,如MARF1、CHGA、BMPR1B、IMMP2L、CDK14、ZDHHC3、CCDC71、DSCAML1、LIMK2、P2RY14等。经GO与KEGG通路分析发现,GO功能显著富集在钠离子跨膜转运蛋白活性的调控、凋亡过程的调控、钠离子通道调节剂活性、G蛋白偶联受体结合、G蛋白偶联嘌呤核苷酸受体活性等条目,KEGG显著富集通路主要与信号传递、信号通路、物质代谢等通路有关。分型结果表明,MARF1基因有11个SNPs位点在皮山红羊群体中真实存在,其中,g.14023542 T＞A、g.14036507 A＞G、g.14046123 C＞T位点与群体平均产羔数显著关联,且前2个突变位点呈现强连锁关系(r²＞0.3),g.14023542 T＞A位点TT基因型具有最多的平均产羔数(1.901±0.675)。【结论】皮山红羊高繁组和低繁组两个群体遗传背景相似,具有一定程度的分化,但分化不明显。MARF1、CHGA、BMPR1B、IMMP2L、CDK14、ZDHHC3、CCDC71、DSCAML1、LIMK2、P2RY14等基因可能是影响皮山红羊产羔性状的候选基因。MARF1基因的3个SNPs位点可作为皮山红羊产羔性状潜在分子选育标记。

关键词: 皮山红羊; 全基因组重测序; 选择信号; 产羔数

Abstract: 【Objective】 Pishan Red sheep is a newly bred prolific breed of sheep distributed in Hotan area of Xinjiang.Based on the whole genome resequencing technology, genetic structure of the population and the selection signal region of litter size traits of Pishan Red sheep were understood at the genome level, and the candidate genes were verified.【Method】 Thirty ewes prolific of Pishan Red sheep with 2-3 lambs born were selected as high fertility group (HF) and 30 prolific Pishan Red sheep ewes with single lambs born were selected as low fertility group (LF).The whole genome of these two populations was re-sequenced.Comprehensive analysis methods such as principal component analysis (PCA), phylogenetic tree, population genetic structure and genome-wide scanning (Fst & θπ) were used to determine candidate regions and further screen candidate genes for lambing traits in Pishan Red sheep.The candidate genes were genotyped by flight mass spectrometry.【Result】 The attenuation curves of linkage disequilibrium (LD) analysis of the high and low fertility groups were similar.The phylogenetic tree showed that the degree of differentiation between the two groups were not obvious.The PCA results showed that the two groups were obviously clustered into a cluster, individuals were out of the group, and their location and relationship were consistent with the evolutionary tree structure and population structure results.The window with both the Top 1% Z(Fst) value and the θπ value were set as the candidate region, and a total of 229 strong selection signals were annotated.The annotated genes in HF and LF groups were 86 and 143, respectively.Among them, 42 candidate genes that might be related to reproductive traits were screened, such as MARF1, CHGA, BMPR1B, IMMP2L, CDK14, ZDHHC3, CCDC71, DSCAML1, LIMK2, P2RY14, etc.Through GO function and KEGG pathway analysis, it was found that the GO significant enrichment terms were in the regulation of sodium ion transmembrane transporter activity, regulation of apoptosis process, sodium ion channel regulator activity, G protein-coupled receptor binding, G protein-coupled purine nucleotide receptor activity and other pathways.The KEGG significant enrichment pathways were mainly related to signal transmission, signal pathway, material metabolism and so on.The results of genotyping showed that 11 SNPs of MARF1 gene existed in the population of Pishan Red sheep and g.14023542 T＞A, g.14036507 A＞G and g.14046123 C＞T loci were significantly associated with the average litter size of the population, and the first two loci showed strong linkage relationship (r²＞0.3), and the TT genotype of g.14023542 T＞A locus had the highest average litter size (1.901±0.675).【Conclusion】 The genetic background of the two groups of high and low fertility groups was similar, and there was a certain degree of differentiation, but the differentiation was not obvious.MARF1, CHGA, BMPR1B, IMMP2L, CDK14, ZDHHC3, CCDC71, DSCAML1, LIMK2, P2RY14 and other genes might be candidate genes affecting the lambing traits in Pishan Red sheep.The three SNPs of MARF1 gene could be used as potential molecular breeding markers for lambing traits of Pishan Red sheep.

Key words: Pishan Red sheep; whole genome resequencing; selection signal; litter size

中图分类号:

S826.8⁺9

石兰, 马梅兰, 木合塔帕·买买提江, 杨会国, 依明·苏来曼. 基于全基因组重测序解析皮山红羊群体遗传结构及产羔数候选基因研究[J]. 中国畜牧兽医, 2024, 51(2): 624-638.

SHI Lan, MA Meilan, MUHETAPA Maimaitijiang, YANG Huiguo, YIMING Sulaiman. Study on the Genetic Structure and Litter Size Candidate Genes of Pishan Red Sheep Population Based on Whole Genome Resequencing[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(2): 624-638.

参考文献

[1] 何宗龙.和田多胎红羊生产性能的研究[D].乌鲁木齐:新疆农业大学,2021. HE Z L.Study on production performance of Hetian multiparous red sheep[D].Urumqi:Xinjiang Agricultural University,2021.(in Chinese)
[2] 何宗龙,侯晨曦,洪文娟,等.和田多胎红羊体尺对体重影响的研究[J].中国草食动物科学,2021,41(1):18-23. HE Z L,HOU C X,HONG W J,et al.Study on the influence of body size on body weight of Hetian Multi-fetal Red sheep[J].China Herbivore Science,2021,41(1):18-23.(in Chinese)
[3] 李旭静,张配颖,锡建中,等.基于全基因组重测序筛选绵羊经济性状候选基因[J].中国畜牧杂志,2022,58(2):59-64. LI X J,ZHANG P Y,XI J Z,et al.Screening of candidate genes related to economic traits based on whole genome resequencing in sheep[J].Chinese Journal of Animal Science,2022,58(2):59-64.(in Chinese)
[4] 陈开旭,郭翠洁,杨帆,等.基于全基因组重测序分析新疆细毛羊遗传多样性[J].新疆农业科学,2023,60(5):1292-1300. CHEN K X,GUO C J,YANG F,et al.Genetic diversity analysis of Xinjiang sheep with fine wool based on wholegenome re-sequencing[J].Xinjiang Agricultural Science,2023,60(5):1292-1300.(in Chinese)
[5] LI H,HANDSAKER B,WYSOKER A,et al.1000 genome project data processing subgroup.The sequence alignment/map format and SAMtools[J].Bioinformatics,2010,25(16):2078-2079.
[6] MCKENNA A,HANNA M,BANKS E,et al.The genome analysis Toolkit:A mapreduce framework for analyzing next-generation DNA sequencing data[J].Genome Research,2010,20(9):1297-1303.
[7] PURCELL S,NEALE B,TODD-BROWN K,et al.PLINK:A tool set for whole-genome association and population-based linkage analyses[J].The American Journal of Human Genetics,2007,81(3):559-575.
[8] RETIEF J D.Phylogenetic analysis using PHYLIP[J].Methods in Molecular Biology,2000,132:243-258.
[9] KALYAANAMOORTHY S,MINH B Q,WONG T K F,et al.ModelFinder:Fast model selection for accurate phylogenetic estimates[J].Nature Methods,2017,14(6):587-589.
[10] 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,2019,35(10):1786-1788.
[11] WANG J J,ZHANG T,CHEN Q M,et al.Genomic signatures of selection associated with litter size trait in Jining Gray goat[J].Frontiers in Genetics, 2020,11:286.
[12] 李恒.利用基因组重测序技术鉴定川中黑山羊多羔性状关键调控基因[D].成都:西南民族大学,2021. LI H.The key regulatory genes of polytocous traits in Chuanzhong Black goats were identified by genome resequencing technology[D].Chengdu:Southwest University of Nationalities,2021.(in Chinese)
[13] 张非.MARF1在仓鼠卵母细胞中的表达与作用研究[D].济南:山东大学,2022. ZHANG F.The expression and function of MARF1 in hamster oocytes[D].Jinan:Shandong University,2022.(in Chinese)
[14] 范业锴.miRNA和lncRNA对绵羊季节性繁殖关键基因表达的调控[D].邯郸:河北工程大学,2022. FAN Y X.Regulation of miRNA and lncRNA on the expression of key genes in seasonal reproduction of sheep[D].Handan:Hebei University of Engineering,2022.(in Chinese)
[15] 高圆圆.蒙古羊和乌珠穆沁羊BMPR1B基因突变位点的挖掘及其与多胎性状的关联性分析[D].呼和浩特:内蒙古大学,2022. GAO Y Y.Excavation of BMPR1B gene mutation sites in Mongolian sheep and Ujumqin sheep and their association with multiple birth traits[D].Hohhot:Inner Mongolia University,2022.(in Chinese)
[16] ZHANG L,ZHAO F,LI C,et al.Hypomethylation of DNA promoter upregulates ADAMTS7 and contributes to HTR-8/SVneo and JEG-3 cells abnormalities in pre-eclampsia[J].Placenta,2020,93:26-33.
[17] 孙文文.SPATA48基因及3个候选miRNA基因的多态性与生精障碍的相关性研究[D].大理:大理大学,2021. SUN W W.Association of polymorphisms of SPATA48 gene and three candidate miRNA genes with spermatogenesis impairment[D].Dali:Dali University,2021.(in Chinese)
[18] JUMEAU F,COM E,LANE L,et al.Human spermatozoa as a model for detecting missing proteins in the context of the chromosome-centric human proteome project[J].Journal of Proteome Research,2015,14(9):3606-3620.
[19] 李秋华,周泽荣,祝晓丽,等.精子表面透明带蛋白受体的分析与功能研究[J].实用医院临床杂志,2020,17(1):20-23. LI Q H,ZHOU Z R,ZHU X L,et al.Analysis and functional study of zona pellucida receptor on surface[J].Journal of Practical Hospital Clinical,2020,17(1):20-23.(in Chinese)
[20] 方俊顺.蛋白质酰基转移酶ZDHHC3在卵母细胞成熟过程中的功能研究[D].北京:中国农业大学,2016. FANG J S.The function of protein acyltransferase ZDHHC3 during oocyte maturation[D].Beijing:China Agricultural University,2016.(in Chinese)
[21] 谷漓芳.Immp2l通过ATF4调节卵巢颗粒细胞炎症性衰老的作用及机制研究[D].银川:宁夏医科大学,2022. GU L F.The role and mechanism of Immp2l in regulating inflammatory senescence of ovarian granulosa cells through ATF4[D].Yinchuan:Ningxia Medical University,2022.(in Chinese)
[22] 杜文凯,张逸寅,杜薇.miR-206通过靶向CDK14抑制雌激素诱导的ER-α36阳性胃癌BGC-823细胞的增殖和侵袭[J].中国肿瘤生物治疗杂志,2021,28(7):689-695. DU W K,ZHANG Y Y,DU W.miR-206 inhibits the proliferation and invasion of estrogen-induced ER-α36-positive gastric cancer BGC-823 cells by targeting CDK14[J].Chinese Journal of Tumor Biotherapy,2021,28(7):689-695.(in Chinese)
[23] 姚玉琛.线粒体电子传递链缺陷的小鼠胚胎干细胞系的构建[D].曲阜:曲阜师范大学,2019. YAO Y C.Construction of mouse embryonic stem cell line with mitochondrial electron transport chain defect[D].Qufu:Qufu Normal University,2019.(in Chinese)
[24] 李燕,阮林浩,索塔林,等.RNF149通过泛素化介导的CD9降解调控细胞增殖[J].生物化学与生物物理进展,2013,40(12):1230-1238. LI Y,RUAN L H,SUO T L,et al.RNF149 regulates the cell proliferation by the polyubiquitination mediated CD9 degradation[J].Progress in Biochemistry and Biophysics,2013,40(12):1230-1238.(in Chinese)
[25] 王月凤.MARF1在斑马鱼卵子发生中的表达及作用研究[D].济南:山东大学,2022. WANG Y F.The expression and function of MARF1 in zebrafish oogenesis[D].Jinan:Shandong University,2022.(in Chinese)
[26] SU Y Q,SUN F,HANDEL M A,et al.Meiosis arrest female 1(MARF1) has nuage-like function in mammalian oocytes[J].Proceedings of the National Academy of Sciences of the United States of America,2012,109(46):18653-18660.
[27] ZHU L,KANDASAMY S K,LIAO S E,et al.LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes[J].Nature Communications,2018,9(1):4031.