连续性纯合片段在畜禽基因组研究中的应用
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刘刚,孙飞舟,朱芳贤,冯海永,韩旭
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Runs of homozygosity and its application on livestock genome study
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Liu Gang,Sun Feizhou,Zhu Fangxian,Feng Haiyong,Han Xu
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| 表1 不同畜禽群体中鉴定ROH设置参数比较 |
| Table 1 Comparison of pre-set parameters for identification and characterization of ROH in different animal species |
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| 物种 | 软件/编程语言 | 每个ROH中
连续SNP数量① | 密度②
(SNP/kb) | 最大间隔③ | 最少长度(kb)④ | 参考文献 | 牛
(Bos taurus) | Fortran 90 | 15 | - | - | 1000 | [4] | | PLINK v 1.07 | 58 | 1/50 | 100 | 500 | [10] | | PLINK v 1.07 | 30 | - | - | - | [53] | | SNP & VARIATION SUITE v 7.6.8 | 15 | 1/1000 | 1000 | 1000 | [5] | | SNP & VARIATION SUITE v 7.6.8 | 50,100 | 1/50 | 250 | 1000 | [11] | | PLINK v 1.07 | - | - | 1000 | - | [54] | | PLINK v 1.07 | 50 | - | - | 1000 | [55] | | SAS 9.2 | 15 | - | 1000 | 1000 | [20] | | PLINK v1.07 | 30 | - | - | 1000 | [56] | | R Development Core team (2018) | - | 1/50 | 100 | 100 | [57] | | SNP & VARIATION SUITE v 7.6.8 | 30 | 1/100 | 500 | 4000 | [58] | | Perl script | 50 | - | - | - | [59] | | PLINK v1.07 | 50 | 1/120 | 1000 | 500 | [60] | | PLINK v1.90 | 50 | 1/100 | 1800 | 3400 | [23] | | PLINK v1.90 | 50 | 1/50 | 500 | 1000 | [61] | | PLINK v1.90 | 20,35,50 | - | - | - | [62] | | vcftools | - | - | - | 500 | [63] | | PLINK v1.90 | 40 | 1/100 | 1000 | 4000 | [24] | | PLINK v1.90 | 10 | - | 1000 | - | [64] | | cgaTOH | 58 | 1/120 | 1000 | 500 | [65] | | SNP & Variation Suite (SVS) | 15 | 1/1000 | 1000 | 1000 | [66] | | PLINK v1.07 | 20 | 1/1000 | - | 10 | [8] | | PLINK v1.07 | - | - | - | 500 | [67] | | 物种 | 软件/编程语言 | 每个ROH中
连续SNP数量① | 密度②
(SNP/kb) | 最大间隔③ | 最少长度(kb)④ | 参考文献 | 猪
(Sus scrofa) | PLINK v1.07 | 20 | 1/1000 | 1000 | 10 | [9] | | SNP & Variation Suite (SVS) | 30 | 1/100 | 100 | 1000 | [68] | | PLINK v1.07 | 10 | 1/500 | 1000 | 5000 | [23] | | Fortran- | 30 | 1/100 | 1000 | - | [24] | | PLINK v1.09 | 50 | 1/50 | - | 1000 | [69] | | PLINK v1.09 | - | - | - | 500 | [25] | | PLINK v1.09 | 40 | - | - | - | [70] | | PLINK v1.07 | 50 | - | - | 500 | [71] | | PLINK v1.07 | 50 | 1/100 | | 1000 | [72] | | PLINK v1.07 | - | - | 250 | 500 | [73] | | PLINK v1.07 | 20 | 1/50 | 500 | - | [33] | 绵羊
(Ovis aries) | SNP & Variation Suite program | 25 | - | 1000 | - | [74] | | PLINK v1.09 | - | 1/100 | 250 | 1000 | [34] | | PLINK v1.09 | - | 1/100 | 1000 | 1000 | [75] | | PLINK v1.09 | 30 | 1/100 | 250 | 1000 | [22] | | PLINK v1.9 | 50 | - | - | 500 | [76] | | PLINK v1.09 | 50 | - | - | - | [77] | | In-house script | 20 | | 500 | 2000 | [37] | 山羊
(Capra hircus) | PLINK v1.09 | 25 | 1/50 | 1000 | 1000 | [78] | | PLINK v1.07 | 50 | 1/50 | 1000 | 500 | [28] | | PLINK v1.07 | 50 | - | - | 400 | [29] | 马
(Equus caballus) | PLINK v1.7 | | 1/50 | 100 | 500 | [30] | | PLINK v1.07 | 100 | 1/50 | 100 | 150 | [31] | | PLINK v1.9 | 20 | 1/50 | 1000 | - | [38] | | PLINK 1.9 | - | 1/100 | - | 1000 | [39] | | 鸡(Gallus gallus) | PLINK 1.9 | - | 1/50 | - | 100 | [40] |
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