Selection signatures in Canchim beef cattle

Ismael Urbinati; Nedenia Bonvino Stafuzza; Marcos Túlio Oliveira; Tatiane Cristina Seleguim Chud; Roberto Hiroshi Higa; Maurício Mello de Alencar; Marcos Eli Buzanskas; Danísio Prado Munari

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Selection signatures in Canchim beef cattle

机译：坎奇姆肉牛的选择签名

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Background:Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels.High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection,known as selection signatures (SS).The SS are detectable by different methods,such as the extended haplotype homozygosity (EHH);and the integrated haplotype score (iHS),which is derived from the EHH.The aim of this study was to identify SS regions in Canchim cattle (composite breed),genotyped with high-density SNP panel.Results:A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control.The iHS statistic for each marker was transformed into piHS for better interpretation of the results.Chromosomes BTA5 and BTA14 showed piHS ＞ 5,with 39 and nine statistically significant SNPs (P＜ 0.00001),respectively.For the candidate selection regions,iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb.We have identified genes that play an important role in metabolism,melanin biosynthesis (pigmentation),and embryonic and bone development.Conclusions:The observation of SS indicates that the selection processes performed in Canchim,as well as in the founder breeds (i.e.Charolais),are maintaining specific genomic regions,particularly on BTA5 and BTA14.These selection signatures regions could be associated with Canchim characterization.

机译：背景技术：基因组学的最新技术发展已使牛可以通过单核苷酸多态性（SNP）面板进行基因分型。高密度SNP面板具有更大的基因组覆盖范围，可用于通过选择而鉴定基因组的保守区域，即选择通过不同的方法可以检测到SS，例如扩展单倍型纯合性（EHH）和源自EHH的综合单倍型评分（iHS）。结果：在进行基因型质量控制后，尚待分析687 655个SNP标记和396个样本，以进行SS分析。每种标记的iHS统计数据被转化为piHS，以便更好地解释染色体BTA5和BTA14的piHS＞ 5，分别具有39个和9个统计学上显着的SNP（P ＜0.00001）。在整个基因组中进行分析并在500 Kb的不重叠窗口内取平均值。我们已经鉴定出在代谢，黑色素生物合成（色素沉着）以及胚胎和骨骼发育中起重要作用的基因。结论：对SS的观察表明选择过程在Canchim以及其创始品种（即夏洛来牛）中进行的研究，都保持了特定的基因组区域，尤其是在BTA5和BTA14上。这些选择标记区域可能与Canchim的鉴定有关。

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《畜牧与生物技术杂志(英文版)》 |2017年第1期|15-23|共9页
作者
Ismael Urbinati; Nedenia Bonvino Stafuzza; Marcos Túlio Oliveira; Tatiane Cristina Seleguim Chud; Roberto Hiroshi Higa; Maurício Mello de Alencar; Marcos Eli Buzanskas; Danísio Prado Munari;
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Departamento de Ci(e)ncias Exatas,-Univ Estadual Paulista, Faculdade de Ci(e)ncias Agrárias e Veterinárias, Jaboticabal, Sāo Paulo 14884 900, Brazil;

Departamento de Ci(e)ncias Exatas,-Univ Estadual Paulista, Faculdade de Ci(e)ncias Agrárias e Veterinárias, Jaboticabal, Sāo Paulo 14884 900, Brazil;

Departamento de Tecnologia, UNESP-Univ Estadual Paulista, Faculdade de Ci(e)ncias Agrárias e Veterinárias, Jaboticabal, Sāo Paulo 14884-900, Brazil;

Departamento de Ci(e)ncias Exatas,-Univ Estadual Paulista, Faculdade de Ci(e)ncias Agrárias e Veterinárias, Jaboticabal, Sāo Paulo 14884 900, Brazil;

Embrapa Agricultural Informatics, Campinas, Sāo Paulo 13083-886, Brazil;

Embrapa Southeast Livestock, Sāo Carlos, Sāo Paulo 13560-970, Brazil;

Departamento de Ci(e)ncias Exatas,-Univ Estadual Paulista, Faculdade de Ci(e)ncias Agrárias e Veterinárias, Jaboticabal, Sāo Paulo 14884 900, Brazil;

Departamento de Ci(e)ncias Exatas,-Univ Estadual Paulista, Faculdade de Ci(e)ncias Agrárias e Veterinárias, Jaboticabal, Sāo Paulo 14884 900, Brazil;

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Selection signatures in Canchim beef cattle

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