基于RAD-seq简化基因组测序估算狼山鸡分子亲缘系数和近交系数
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摘要
为准确度量狼山鸡保种群体的近交统计量,并比较不同算法在近交统计量度量中的可靠性,研究以国家级地方鸡种基因库保存的狼山鸡为研究对象,通过RAD-seq简化基因组测序获得高密度SNP信息,并计算两种分子亲缘系数(kin1和kin2)和四种分子近交系数(F_(ROH)、F_(GRM)、F_(HOM)和F_(UNI))。结果表明:kin1对系谱记录中全同胞、半同胞的检出率较高(93/117);F_(GRM)、F_(HOM)和F_(UNI)三种分子近交系数两两之间极显著相关(P<0.01),F_(ROH)(F_(ROH)>100、F_(ROH)>1 000和F_(ROH)>3 000)与F_(GRM)、F_(HOM)和F_(UNI)的相关系数较低,仅F_(ROH)>100与F_(HOM)达到极显著正相关(P<0.01)。基于高密度SNPs估算的kin1为较准确的狼山鸡分子亲缘系数,可用于狼山鸡保种群的系谱校正;高密度SNP标记有利于检测到短的ROH,同时提高FROH与F_(GRM)、F_(HOM)和F_(UNI)的正相关性。
In order to get the inbreeding statistics of Langshan chicken accurately, and compare different methods performed for the estimation of genomic inbreeding parameters, Langshan chicken preserved in the National Chicken Genetic Resources were selected, and their SNP markers were obtained by RAD-seq. Two genomic kinship coefficients(kin1 and kin2) and four genomic inbreeding coefficients(F_(ROH), F_(GRM), F_(HOM) and F_(UNI)) were calculated. Combined with pedigree information, the results showed that kin1 had a higher detection rate for full siblings and half siblings(93/117).Highly significant correlations(P<0.01) were found among the molecular inbreeding coefficients(F_(GRM), F_(HOM) and F_(UNI)).The correlation coefficients of F_(ROH)(F_(ROH)>100, F_(ROH)>1 000 and F_(ROH)>3 000) were low with F_(GRM), F_(HOM) and F_(UNI), and only significant correlation was found between F_(ROH)>100 and F_(HOM)(P<0.01). Therefore, kin1, calculated based on high-density SNP markers,was a relatively accurate estimate of the kinship coefficients in Langshan chicken, which could be used for pedigree correction. High-density SNP markers was conducive to detection of short ROH, which meanwhile increased the positive correlation between F_(ROH) and F_(GRM), between F_(HOM) and F_(UNI).
In order to get the inbreeding statistics of Langshan chicken accurately, and compare different methods performed for the estimation of genomic inbreeding parameters, Langshan chicken preserved in the National Chicken Genetic Resources were selected, and their SNP markers were obtained by RAD-seq. Two genomic kinship coefficients(kin1 and kin2) and four genomic inbreeding coefficients(F_(ROH), F_(GRM), F_(HOM) and F_(UNI)) were calculated. Combined with pedigree information, the results showed that kin1 had a higher detection rate for full siblings and half siblings(93/117).Highly significant correlations(P<0.01) were found among the molecular inbreeding coefficients(F_(GRM), F_(HOM) and F_(UNI)).The correlation coefficients of F_(ROH)(F_(ROH)>100, F_(ROH)>1 000 and F_(ROH)>3 000) were low with F_(GRM), F_(HOM) and F_(UNI), and only significant correlation was found between F_(ROH)>100 and F_(HOM)(P<0.01). Therefore, kin1, calculated based on high-density SNP markers,was a relatively accurate estimate of the kinship coefficients in Langshan chicken, which could be used for pedigree correction. High-density SNP markers was conducive to detection of short ROH, which meanwhile increased the positive correlation between F_(ROH) and F_(GRM), between F_(HOM) and F_(UNI).
引文
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[3]KARDOS M,LUIKART G,ALLENDORF F W.Measuring individual inbreeding in the age of genomics:Markerbased measures are better than pedigrees[J].Heredity,2015,115(1):63-72.
[4]HOFFMAN J I,SIMPSON F,DAVID P,et al.Highthroughput sequencing reveals inbreeding depression in a natural population[J].Proceedings of the National Academy of Sciences,2014,111(10):3775-3780.
[5]HAMMERLY S C,MORROW M E,JOHNSON J A.Acomparison of pedigree-and DNA-based measures for identifying inbreeding depression in the critically endangered Attwater′s Prairie-chicken[J].Molecular Ecology,2013,22(21):5313-5328.
[6]王孝义,李明丽,胡伟,等.基于SNP的基因组近交系数衡量群体遗传多样性的准确性[J].云南农业大学学报(自然科学),2017(5):74-80.
[7]张静静,高会江,吴洋,等.利用SNP标记估计西门塔尔牛亲缘系数的准确性[J].畜牧兽医学报,2016,47(2):268-275.
[8]DANECEK P,AUTON A,ABECASIS G,et al.The variant call format and VCFtools[J].Bioinformatics,2011,27(15):2156-2158.
[9]YANG J,BENYAMIN B,MCEVOY B P,et al.Common SNPs explain a large proportion of the heritability for human height[J].Nature Genetics,2010,42(7):565-569.
[10]MANICHAIKUL A,MYCHALECKYJ J C,RICH S S,et al.Robust relationship inference in genome-wide association studies[J].Bioinformatics,2010,26(22):2867-2873.
[11]PURCELL S,NEALE B,TODDBROWN K,et al.PLINK:A tool set for whole-genome association and populationbased linkage analyses[J].American Journal of Human Genetics,2007,81(3):559-575.
[12]YANG J,LEE S H,GODDARD M E,et al.GCTA:Atool for genome-wide complex trait analysis[J].American Journal of Human Genetics,2011,88(1):76-82.
[13]VANRADEN P M.Efficient methods to compute genomic predictions[J].Journal of Dairy Science,2008,91(11):4414-4423
[14]WRIGHT S.Coefficients of inbreeding and relationship[J].The American Naturalist,1922,56(645):330-338.
[15]DAVEY J W,BLAXTER M L.RADSeq:Next-generation population genetics[J].Briefings in Functional Genomics,2010,9(5-6):416-423.
[16]王洪志,李国辉,张贤,等.基于RAD-seq简化基因组测序评价鹿苑鸡不同保种群保种现状[J].畜牧兽医学报,2017,48(5):818-825.
[17]ZHANG Q,CALUS M P,GULDBRANDTSEN B,et al.Estimation of inbreeding using pedigree,50k SNP chip genotypes and full sequence data in three cattle breeds[J].BMC Genetics,2015(16):88.
[18]MIRNA K,RUTH M Q,FRANKLIN C S,et al.Genomic Runs of Homozygosity Record Population History and Consanguinity[J].PLoS One,2010,5(11):e13996.
[19]PURFIELD D C,BERRY D P,SINEAD M P,et al.Runs of homozygosity and population history in cattle[J].BMC Genetics,2012,13(1):70.
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