蒙古羊不同尾椎数相关选择信号的挖掘研究
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摘要
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。
To reveal the molecular mechanism underlining the caudal vertebra formation, the genome-wide selection signal, the related genes of Mongolian sheep tail length traits and the possible mutation sites were detected by comparing the genetic differentiation level of Mongolian sheep population with different numbers of tail vertebrae. Based on whole genome resequencing data, the selection signal of caudal vertebra was screened with the genetic differentiation coefficient(Fst) and genetic diversity ratio(pi ratio) between the two sheep groups. A chromosome region with higher Fst and pi ratio value were selected as a candidate region. A total of 76 selected regions were found ultimately, which belonged to the QTL of tail fat deposition and skeletal development. GO and pathway analysis of the 63 genes contained in these candidate regions found the enrichment of Wnt and FGF signaling pathways related to bone regeneration, and the functional candidate genes such as LRP6 were also found. In summary, we identified the selected regions associated with the number of caudal vertebrae, suggesting that the formation of Mongolian sheep populations with different numbers of caudal vertebrae may be caused by one or more mutations in non-gene coding regions.
To reveal the molecular mechanism underlining the caudal vertebra formation, the genome-wide selection signal, the related genes of Mongolian sheep tail length traits and the possible mutation sites were detected by comparing the genetic differentiation level of Mongolian sheep population with different numbers of tail vertebrae. Based on whole genome resequencing data, the selection signal of caudal vertebra was screened with the genetic differentiation coefficient(Fst) and genetic diversity ratio(pi ratio) between the two sheep groups. A chromosome region with higher Fst and pi ratio value were selected as a candidate region. A total of 76 selected regions were found ultimately, which belonged to the QTL of tail fat deposition and skeletal development. GO and pathway analysis of the 63 genes contained in these candidate regions found the enrichment of Wnt and FGF signaling pathways related to bone regeneration, and the functional candidate genes such as LRP6 were also found. In summary, we identified the selected regions associated with the number of caudal vertebrae, suggesting that the formation of Mongolian sheep populations with different numbers of caudal vertebrae may be caused by one or more mutations in non-gene coding regions.
引文
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[2]何小龙,王位,王艳欣,等.蒙古羊尾椎数与尾型变异分析[J].黑龙江畜牧兽医,2017(15):102-105.
[3]谢成侠.中国养牛羊史[M].北京:农业出版社,1985.
[4]甘尚权,张伟,沈敏,等.绵羊X染色体59383635位点多态性与脂尾性状的相关性分析[J].遗传,2013,35(10):1209-1216.
[5]LI H,DURBIN R.Fast and accurate short read alignment with Burrows-Wheeler transform[J].Bioinformatics,2009,25(14):1754-1760.
[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]COCKERHAM C C,WEIR B S.Covariances of relatives stemming from a population undergoing mixed self and random mating[J].Biometrics,1984,40(1):157-164.
[8]袁泽湖.利用选择信号分析方法筛选与绵羊尾型相关的基因[D].北京:中国农业科学院,2016.
[9]WANG X,ZHOU G,XU X,et al.Transcriptome profile analysis of adipose tissues from fat and short-tailed sheep[J].Gene,2014,549(2):252-257.
[10]MORADI M H,NEJATI-JAVAREMI A,MORADI-SHAHRBABAK M.Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition[J].BMC Genetics,2012(13):10.
[11]刘真,王慧华,刘瑞凿,等.不同尾型绵羊全基因组选择信号检测[J].畜牧兽医学报,2015,46(10):1721-1732.
[12]刘艳玲,李方兵,赵曦.Wnt信号通路在成骨细胞中的作用:成骨还是破骨?[J].中国组织工程研究,2014,18(33):5366-5371.
[13]MCLAUGHLIN K A,LEVIN M.Bioelectric signaling in regeneration:Mechanisms of ionic controls of growth and form[J].Developmental Biology,2018,433(2):177-189.
[14]LIN G,SLACK J M.Requirement for Wnt and FGF signaling in Xenopus tadpole tail regeneration[J].Developmental Biology,2008,316(2):323-335.
[15]ARYA M,JAYARAM R,HE W,et al.LRP6 mutation in a family with early coronary disease and metabolic risk factors[J].Science,2007,315(5816):1278-1282.
[16]LI C,WILLIAMS B O,CAO X,et al.LRP6 in mesenchymal stem cells is required for bone formation during bone growth and bone remodeling[J].Bone Research,2014,2(1):43-54.