共查询到18条相似文献，搜索用时 656 毫秒
1.
通过对比不同尾椎数的蒙古绵羊群体在基因组上的遗传分化水平,对全基因组选择信号、蒙古羊尾长性状的相关基因及可能的突变位点进行检测,试图解析尾椎形成的分子机制。基于全基因组重测序数据,使用两组群间的遗传分化系数(Fst)和遗传多样性比率(pi ratio)检测尾椎选择信号,将Fst值和pi ratio较大的染色体区段作为受选择候选区域。结果表明,共找到76个选择区域,这些区域分别落在了尾脂肪沉积和骨骼发育的QTL上,进一步对这些候选区域所包含的63个基因进行基因功能及通路的注释分析,富集到骨骼再生相关的Wnt和FGF信号通路,同时发现LRP6等功能候选基因。该研究确定了与尾椎数相关的受选择区域,推测不同尾椎数蒙古绵羊群体的形成可能由非基因编码区域的一个或者多个突变造成。 相似文献
2.
旨在研究德国肉用美利奴羊基因组选择信号。利用绵羊高密度SNPs芯片,运用iHS方法检测德国肉用美利奴羊基因组选择信号,并通过生物信息学分析揭示其潜在受选择基因。选择信号检测结果表明,在全基因组范围内共检测到220个具有选择信号的基因组区段,这些区段内与895个候选基因紧密相关。基因富集结果表明,这些基因主要与蛋白翻译、骨骼发育、生物合成调控、肌肉器官发育、视黄酸受体活性、转录因子结合、核糖体组分等相关。研究结果为充分利用德国肉用美利奴羊的种用价值以及高效开展该品种羊的群体改良工作提供了参考依据。 相似文献
3.
为了分析盆周山地猪群体的选择信号，本研究利用猪50K基因芯片，运用Tajima’s D方法分析盆周山地猪群体基因组上受选择的信号区域，并通过生物信息学分析筛选受选择的候选基因。结果表明，盆周山地猪群体基因组上受选择的区域有252个，这些区域共包含267个候选基因，其中，在猪上已注释的基因184个，如免疫性状相关基因MYO1G、CD86、IKF2，肉质性状相关基因PRKAG3、PRDM16、SND1，繁殖性状相关基因FSHR、LTF、AP3B1和生长性状相关基因SREBF2、SDC3、SLIT3。候选基因GO功能富集表明，这些基因参与了机体的免疫、行为、心管发育等生物学进程。KEGG信号通路分析发现，部分基因可能与催产素信号通路相关。本研究首次构建了盆周山地猪全基因组水平上的选择信号图谱，筛选了受选择的重要经济性状候选基因，研究结果为更好地保护、开发和利用盆周山地猪奠定了理论基础。 相似文献
4.
选择信号是生物群体在选择进化的过程中,由于选择作用使得生物群体表型特征发生变化的对应基因组信息。本研究基于嵊县花猪等10个中外地方猪品种共计517个个体全基因组测序数据,利用群体分化指数(F_(ST))和核苷酸多态性(θ_π)方法检测嵊县花猪群体与浙江省其他地方猪种群体间以及与西方猪种群体间的选择信号,找到17个落入选择信号区域的候选基因。其中与浙江省地方猪群体相比,检测出候选基因9个,分别是SYT1、FAM135B、GLIS1、GALNT2、BIN1、LOC100627093、TG、SOX9、CH25H;与西方猪群体相比,检测出候选基因8个,分别是MGAT5、MAPK4K4、KSR2、RBP5、HDLBP、KCNE2、KIRREL3、BTBD11。这些候选基因在脂肪代谢、免疫、胚胎发育、消化代谢等通路中发挥重要的作用,说明嵊县花猪在耐粗饲、抗病力强、高繁殖力等性状上经历了人工选择,为研究嵊县花猪的群体特征提供了参考价值。 相似文献
5.
恩施黑猪基因组群体遗传学参数的估计与选择信号研究 总被引：1，自引：1，他引：0
旨在调查恩施黑猪基因组群体遗传学参数与选择信号。本研究利用Porcine 80K SNP芯片,通过计算亲缘系数、近交系数、连锁不平衡程度与有效群体大小等群体遗传学层面的参数评估恩施黑猪种群结构关系,运用CLR和iHS方法检测恩施黑猪基因组选择信号,并通过生物信息学分析揭示其潜在受选择基因。亲缘系数计算发现,咸丰县恩施黑猪个体间平均亲缘系数为0.12;近交系数计算表明, 16%的样本近交系数大于0.125,存在明显近交累积。此外,本研究构建了恩施黑猪全基因组连锁不平衡图谱;利用连锁不平衡信息,恩施黑猪估计历史有效群体大小呈现逐代下降趋势,其中5世代前有效群体大小约为25头。基于CLR方法共检测到126个显著选择信号候选区域,总长约为51.6 Mb,占基因组总长的2.1%。利用iHS方法,共发现248个显著选择信号候选区域,长度约为78.78 Mb,约占基因组总长的3.2%。富集分析表明,与选择信号区域重叠的LPAR2、NDUFA13、MEF2B、AHR基因分别与胴体长度(滴水损失)、精子形成、骨骼肌分化和总产仔数相关。研究表明,现存恩施黑猪群体血统较窄,近交累积严重,有效群体大小较小,并呈现继续缩小的趋势。选择信号分析揭示的一系列潜在受选择基因能够为未来恩施黑猪的遗传改良提供一定的参考依据。 相似文献
6.
【目的】阐明晋南牛的遗传结构特征，通过选择信号检测挖掘与晋南牛经济性状相关的候选基因，探究其在进化过程中的受选择情况。【方法】对晋南牛和红安格斯牛全基因组测序数据进行分析，鉴定2个群体的单核苷酸多态性(single nucleotide polymorphism, SNP)标记，分析其在基因组的位置及其结构特征，基于SNP信息进行主成分分析(PCA)、构建状态同源矩阵(IBS);采用群体遗传分化指数(Fst)和核苷酸多样性比值(θπ)方法联合筛选晋南牛基因组受到强烈选择的区域，并对筛选到的受选择基因进行数量性状基因座(QTL)定位、GO功能和KEGG通路富集分析。【结果】晋南牛群体SNPs位点主要分布于基因间区域，其次位于内含子区域。PCA和IBS分析结果表明，晋南牛和红安格斯牛2个群体间不存在杂交现象，且晋南牛群体中个体间遗传距离较远。通过Fst和θπ联合分析共筛选到188个潜在受选择区域。QTL分析结果表明晋南牛的选择信号多与生长、肉质及抗病性状相关。GO功能和KEGG通路富集分析显示，筛选到晋南牛强受选择的与经济性状相关的候选基因11个... 相似文献
7.
【目的】试验旨在揭示终端父本皮特兰猪与杜洛克猪在人工选择作用下重要经济性状呈现出表型趋同的基因组变化特征。【方法】利用376头皮特兰猪、451头杜洛克猪品系Ⅰ、841头杜洛克猪品系Ⅱ和497头杜洛克猪品系Ⅲ群体的50K SNP芯片数据,以100 kb窗口、50 kb步长计算综合单倍型评分(iHS)和等位基因频率差(△AF),分别取前5%作为猪群体内、群体间的基因组选择信号候选区域;利用bedtools分别对iHS、△AF按照左右200 kb进行合并,每2个群体间合并后的iHS、△AF统计量的重叠区域定义为性状趋同区域,并挖掘该区域与猪重要经济性状相关的平行选择信号。【结果】iHS结果显示,在皮特兰猪和杜洛克猪4个群体内共检测到5 112个选择信号候选区域,总长约487.51 Mb。基于△AF方法,于皮特兰猪和杜洛克猪每2个群体间共检测到9 579个选择信号显著区域,总长约913.50 Mb。基于合并后的iHS和△AF,共检测到52个性状趋同区域,总长约4.67 Mb,注释到88个与猪的繁殖、胴体和肉质等性状相关的平行选择候选基因。【结论】皮特兰猪和杜洛克猪群体间存在性状趋同的基因组选择区域有52个,平行选择信号主要涉及猪的繁殖、胴体及肉质等重要经济性状,这与瘦肉型猪种相同的育种方向相关,这些关键基因的发现可为后续商业猪品种遗传改良提供参考。 相似文献
8.
【目的】利用选择信号分析方法在伊犁鹅和霍尔多巴吉鹅中筛选与产蛋性状相关的候选基因。【方法】选取健康状况良好、饲养管理水平一致的2岁伊犁鹅母鹅和霍尔多巴吉鹅母鹅各24只,采集血液样本,提取基因组DNA,利用全基因组重测序技术进行选择信号检测分析,筛选出受到选择的候选区域,针对注释基因进行GO功能和KEGG通路富集分析,进一步筛选出与鹅产蛋性状相关的候选基因。【结果】全基因组重测序的平均测序深度为15.28×,与参考基因组比对率在97.31%以上。通过群体分化指数(Fst)对伊犁鹅和霍尔多巴吉鹅2个群体进行分析,共筛选到1 231个候选区域。与核苷酸多样性(Pi)进行联合分析后,伊犁鹅群体共筛选出10个候选区域,得到5个注释基因;霍尔多巴吉鹅群体中共筛选出353个候选区域,得到263个注释基因。GO功能和KEGG通路富集分析发现,初步筛选出6个可能与鹅产蛋性状相关的候选基因(BMP2、BMP6、MIS、ENO1、LIF、EP300),还发现了IL-18基因可能与禽类的免疫有关。【结论】本研究筛选出6个可能与鹅产蛋性状相关的候选基因,为揭示鹅产蛋性状的分子调控机制提供了参考。 相似文献
9.
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(πratio)进行全基因组选择性清除分析,取top 5%Fst和πratio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、... 相似文献
10.
基于表型信息和谱系信息估计基因加性效应值的种畜遗传评定方法在家畜遗传改良中发挥了很大作用,但因其无法真正了解控制经济性状的遗传本质,影响了家畜遗传改良的进一步进展。分子标记辅助选择可在一定程度上提高种畜遗传评定准确性,但在目前不能精确定位QTL或基因时,其效率受到很大影响。提高种畜遗传评定准确性的最有效途径应是直接利用控制经济性状的基因,后基因组时代的功能基因组研究的快速发展为实现这一目标提供了契机。同时,多个家畜品种基因组测序完成和大量SNP多态性的发现,使得利用覆盖全基因组多态性标记信息的基因组选择方法为家畜遗传评定开拓了又一条途径。 相似文献
11.
The economic traits of livestock has been significantly improved due to long-term under natural and artificial selection,and the specific variation characterizations emerged from the selected genome regions.As time goes on,the some polymorphism frequency of gene has dropped or disappeared,and keep in a group contains a single haploid type of multiple genes.This frequency variation of gene in specific region on the genomes is called the signatures of selection.Identifying signatures of selection can provide a straightforward insight into the mechaism of domestication and further uncover the casual genes related to the phenotypic variation.The high density SNP chips and large scale resequencing technology have been successfully applied to genomic selection signature in livestock breeds.The methods to detect selection signatures can be classed into three categories:Site frequency spectrum based methods,haplotyped based methods and population differentiation based methods.In the present article,we summarized the methods of selection signature detection and development and application of genomic selection signature methods in livestock.It will provide useful information for researchers working with breeding and evolutionary biology. 相似文献
12.
为了满足人们对畜产品需求的快速增长，必须在加快畜禽产业发展的同时把对环境的影响降到最低，提高畜禽遗传特性有望促进这一问题的解决。进入21世纪以来，以基因组选择为核心的分子育种技术迎来了发展机遇，利用该技术可实现早期准确选择，从而大幅度缩短世代间隔，加快群体遗传进展，并显著降低育种成本。虽然在某些畜种中（如奶牛），基因组选择取得了成功，群体也获得较大遗传进展，但仍无法满足快速增长的需求。因此，亟需寻找能够进一步加快遗传进展的方法。研究表明，在SNP标记数据中加入目标性状的已知功能基因信息，可以提高基因组育种值预测的准确性，进而加快遗传进展。而挖掘更多基因组信息的同时，开发更优化的分析方法可以更有助于目标的实现。文章总结了主要畜禽物种的可用基因组数据，包括牛、绵羊、山羊、猪和鸡以及这些数据是如何有助于鉴定影响重要性状的遗传标记和基因，从而进一步提高基因组选择的准确性。 相似文献
13.
Wheeler MB 《Journal of animal science》2003,81(Z3):32-37
The introduction of specific genes into the genome of farm animals and its stable incorporation into the germ line has been a major technological advance in agriculture. Transgenic technology provides a method to rapidly introduce "new" genes into cattle, swine, sheep, and goats without crossbreeding. It is a more extreme methodology, but in essence, not really different from crossbreeding or genetic selection in its result. Methods to produce transgenic animals have been available for more than 20 yr, yet recently lines of transgenic livestock have been developed that have the potential to improve animal agriculture and benefit producers and/or consumers. There are a number of methods that can be used to produce transgenic animals. However, the primary method to date has been the microinjection of genes into the pronuclei of zygotes. This method is one of an array of rapidly developing transgenic methodologies. Another method that has enjoyed recent success is that of nuclear transfer or "cloning." The use of this technique to produce transgenic livestock will profoundly affect the use of transgenic technology in livestock production. Cell-based, nuclear transfer or cloning strategies have several distinct advantages for use in the production of transgenic livestock that cannot be attained using pronuclear injection of DNA. Practical applications of transgenesis in livestock production include enhanced prolificacy and reproductive performance, increased feed utilization and growth rate, improved carcass composition, improved milk production and/or composition, and increased disease resistance. One practical application of transgenics in swine production is to improve milk production and/or composition. To address the problem of low milk production, transgenic swine over-expressing the milk protein bovine alpha-lactalbumin were developed and characterized. The outcomes assessed were milk composition, milk yield, and piglet growth. Our results indicate that transgenic overexpression of milk proteins may provide a means to improve swine lactation performance. 相似文献
14.
Salvatore Mastrangelo Slim Ben Jemaa Elena Ciani Gianluca Sottile Angelo Moscarelli Mekki Boussaha Marina Montedoro Fabio Pilla Martino Cassandro 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2020,137(6):609-621
The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (FST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock. 相似文献
15.
畜禽的选种选育在生产中至关重要,育种值估计是选种选育的核心。基因组选择（genomic selection,GS）是利用全基因组范围内的高密度标记估计个体基因组育种值的一种新型分子育种方法,目前已在牛、猪、鸡等畜禽育种中得到应用并取得了良好的效果。该方法可实现畜禽育种早期选择,降低测定费用,缩短世代间隔,提高育种值估计准确性,加快遗传进展。基因组选择主要是通过参考群体中每个个体的表型性状信息和单核苷酸多态性（single nucleotide polymorphism,SNP）基因型估计出每个SNP的效应值,然后测定候选群体中每个个体的SNP基因型,计算候选个体的基因组育种值,根据基因组育种值的高低对候选群体进行合理的选择。随着基因分型技术快速发展和检测成本不断降低,以及基因组选择方法不断优化,基因组选择已成为畜禽选种选育的重要手段。作者对一些常用的基因组选择方法进行了综述,比较了不同方法之间的差异,分析了基因组选择存在的问题与挑战,并展望了其在畜禽育种中的应用前景。 相似文献
16.
Selection and breeding are very important in production of livestock and poultry,and breeding value estimation is the core of selection and breeding.Genomic selection (GS) is a novel molecular breeding method to estimate genomic breeding value using high-density markers across the whole genome.At present,GS has been successfully applied in cattle,pig,chicken and so on,and made significant progress.This method can achieve early selection,decrease the testing costs,shorten generation interval,improve the accuracy of breeding value estimation and accelerate genomic progress.GS estimates the effect of SNP by phenotype information and SNP genotype of each individual in the reference population,and measures the SNP genotype to calculate the genomic estimated breeding value in the candidate population,then selects the best individuals according to the genomic estimated breeding value.With the rapid development of genotyping technology and the decrease of detection cost,and the continuous optimization and high efficiency of genomic selection methods,genomic selection has become an important research method in the selection and breeding of livestock and poultry.The authors reviewed some of the widely used genomic selection methods,compared the differences between different methods,analyzed the problems and challenges of genomic selection,and looked forward to its application prospects in breeding. 相似文献
17.
P.G. Eusebi O. Cortés C. Carleos S. Dunner J. Cañon 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2018,135(3):170-177
The identification of genomic regions including signatures of selection produced by domestication and its subsequent artificial selection processes allows the understanding of the evolution of bovine breeds. Although several studies describe the genomic variability among meat or milk production cattle breeds, there are limited studies orientated towards bovine behavioural features. This study is focused on mapping genomic signatures of selection which may provide insights of differentiation between neutral and selected polymorphisms. Their effects are studied in the Lidia cattle traditionally selected for agonistic behaviour compared with Spanish breeds showing tamed behaviour. Two different approaches, BayeScan and SelEstim, were applied using genotypic 50K SNP BeadChip data. Both procedures detected two genomic regions bearing genes previously related to behavioural traits. The frequencies of the selected allele in these two regions in Lidia breed were opposite to those found in the tamed breeds. In these genomic regions, several putative genes associated with enriched metabolic pathways related to the behavioural development were identified, as neurochondrin gene (NCDN) or glutamate ionotropic receptor kainate type subunit 3 (GRIK3) both located at BTA3 or leucine‐rich repeat and Ig domain containing 2 (LINGO2) and phospholipase A2‐activating protein (PLAA) at BTA8. 相似文献
18.
全基因组测序在畜禽中应用的研究进展 总被引：1，自引：0，他引：1
在基因组研究方面,目前全基因组测序已由第一代测序技术发展到第三代测序技术,全基因组测序与传统方法相比具有更加全面、精准、高效等优势。随着测序技术的发展和费用的降低,全基因组测序（whole genome sequencing,WGS）技术逐渐成为基因组研究应用最广泛的技术。全基因组测序已经在畜禽起源进化、重要经济性状基因挖掘、分子育种等方面取得了诸多成果。通过全基因组重测序,能够发现拷贝数变异（copy number variation,CNV）及单核苷酸多态性（single nucleotide polymorphism,SNP）变异,丰富现有的CNV和SNP数据库,为抗病、生长、食欲、代谢调节、表型、环境适应机制及重要经济性状基因的分析提供重要数据。作者针对全基因组测序技术在主要畜禽上的研究进展,综述了全基因组测序在畜禽的品种遗传多样性、群体演变机制、功能基因挖掘等研究中的应用,并探讨了全基因组测序存在的问题,旨在为畜禽种质资源保护和分子育种实践提供参考。 相似文献