巴马香猪全基因组拷贝数变异的检测及其与五块四肢骨骼长度的关联分析

发布时间：2018-04-12 17:52

本文选题：猪 + 巴马香猪　；参考：《江西农业大学》2017年硕士论文

【摘要】：拷贝数变异(copy number variation,CNV)是一种结构变异,具有可遗传性、相对稳定性和高度异质性,并以多种形式广泛地存在基因组范围内。前人的研究显示CNV与畜禽的健康状况、生产性能等密切相关。猪作为一种非常重要的农业动物,对其进行CNV检测及其与生产性状的关联分析具有重要意义。目前,对猪CNV的检测大部分是基于Illumina公司推出的猪60K SNP芯片。由于60K芯片的标记密度相对比较低,相邻标记之间的间隔较大,导致CNV的检测效率较低。本研究利用Affymatrix公司定制的1.4M SNP芯片数据,采用PennCNV和R-GADA两种软件,对中国地方猪种巴马香猪进行CNV检测,并把相互重叠的CNV所在的区域称为(copy number variation region,CNVR)。PennCNV软件共检测到了6237个CNV,它们构成了795个CNVR。R-GADA软件共检测到3489个CNV,它们构成了340个CNVR,其中226个CNVR与PennCNV一致。本研究还考察了不同标记密度对拷贝数检测率的影响。随着SNP密度的增加,CNV的检测率不断上升。因此,1.4M SNP标记没有达到标记饱和的程度,增加标记,还可以进一步提高CNV的检测率。最后将检测到的CNVR与肩胛骨、臂骨、前臂骨、股骨和小腿骨5块四肢骨骼长度进行关联分析,在2、5和7号等染色体上共检测到18个与四肢骨骼长度显著关联(P0.05)的CNVR。本研究利用1.4M高密度SNP芯片的数据对巴马香猪进行CNV检测,绘制了巴马香猪CNVR图谱。在1.4M SNP标记的基础上增加标记,还可以进一步提高CNV的检测率。通过关联分析,鉴定了18个与四肢骨骼长度显著关联的CNVR。本研究结果为巴马香猪品种特异性研究以及四肢骨骼长度的分子育种提供了重要参考。
[Abstract]:Copy number variation (number) is a structural variation with heritability, relative stability and high heterogeneity, and exists in a wide range of genomes in a variety of forms.Previous studies have shown that CNV is closely related to the health status and production performance of livestock and poultry.As a very important agricultural animal, it is of great significance to detect pig by CNV and to analyze its association with production traits.At present, the detection of pig CNV is mostly based on 60 K SNP chip produced by Illumina.Because the labeling density of 60K chip is relatively low and the interval between adjacent markers is large, the detection efficiency of CNV is low.In this study, using the 1.4 M SNP chip data customized by Affymatrix Company, using two kinds of software, PennCNV and R-GADA, we detected the CNV of Chinese local pig Bama Xiang pig.The overlapping region of CNV is called copy number variation region CNVRV. PennCNV software detects 6237 CNVs, and they make up 795 CNVR.R-GADA softwares to detect a total of 3489 CNVs, and they constitute 340 CNVs, of which 226 CNVR are consistent with PennCNV.The effect of different labeling density on copy number detection rate was also investigated.The detection rate of SNP is increasing with the increase of density.Therefore, 1.4m SNP marker did not reach the saturation level, and the detection rate of CNV could be further improved by adding the marker.Finally, the detected CNVR was correlated with the bone length of 5 limbs, such as scapula, arm, forearm, femur and leg. A total of 18 CNVRs with significant association with limb bone length (P0.05) were detected on chromosome 2Q5 and chromosome 7.In this study, the data of 1.4 M high density SNP chip were used to detect the CNV of Bama Xiang pig, and the CNVR map of Bama Xiang pig was plotted.The detection rate of CNV can be further improved by adding the tag on the basis of 1.4m SNP marker.By association analysis, 18 CNVRs with significant association with limb bone length were identified.The results of this study provide important references for the study of breed specificity and molecular breeding of limb bone length in Bama Xiang pig.
【学位授予单位】：江西农业大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S828

【参考文献】