Scholarlink

<p>Genotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate whether the inclusion of genotypes from the founder breeds Nelore (NE) and Charolais (CH) improves the imputation accuracy in the composite beef cattle breed Canchim (CA). The populations studied consisted of 804 NE, 897 CH, and 392 CA animals, all genotyped using high-density panels (777,962 SNP – single nucleotide polymorphisms). CA animals had their genotypes masked to simulate a medium-density panel (54,609 SNP). Fourteen imputation scenarios were evaluated, varying according to breed, sex, year of birth, and lineage. Imputation accuracy was determined based on the percentage of correctly imputed genotypes (PERC) and the squared Pearson’s correlation between observed and imputed genotypes (R<sup>2</sup>). PERC values ranged from 66.52% to 97.39% and R² from 0.6352 to 0.9780. The scenarios that included NE, CH, and CA (males or animals born before 2004) as the reference population for imputing CA females or CA animals born after 2004 showed the highest imputation accuracies. Therefore, the use of founder breeds in the reference population improves the accuracy of genotype imputation in CA cattle. The results indicate that a multibreed reference population, incorporating founder breeds, could provide a more robust and informative genetic basis for imputing composite cattle.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Effect of founder breeds on genotype imputation accuracy in Canchim cattle

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月16日

查看全文
  • Roney Teixeira,
  • Maria Victória Henrique Genuíno,
  • Ayrton Fernandes de Oliveira Bessa,
  • Giovanna Maria dos Santos Câmara,
  • Ana Carolina de Jesus Oliveira,
  • Josineudson Augusto II de Vasconcelos Silva,
  • Lucio Flavio Macedo Mota,
  • Fernando Baldi,
  • Luciana Correia de Almeida Regitano,
  • Cintia Righetti Marcondes,
  • Priscila Arrigucci Bernardes,
  • Donagh Pearse Berry,
  • Danísio Prado Munari,
  • Marcos Eli Buzanskas

摘要

Genotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate whether the inclusion of genotypes from the founder breeds Nelore (NE) and Charolais (CH) improves the imputation accuracy in the composite beef cattle breed Canchim (CA). The populations studied consisted of 804 NE, 897 CH, and 392 CA animals, all genotyped using high-density panels (777,962 SNP – single nucleotide polymorphisms). CA animals had their genotypes masked to simulate a medium-density panel (54,609 SNP). Fourteen imputation scenarios were evaluated, varying according to breed, sex, year of birth, and lineage. Imputation accuracy was determined based on the percentage of correctly imputed genotypes (PERC) and the squared Pearson’s correlation between observed and imputed genotypes (R2). PERC values ranged from 66.52% to 97.39% and R² from 0.6352 to 0.9780. The scenarios that included NE, CH, and CA (males or animals born before 2004) as the reference population for imputing CA females or CA animals born after 2004 showed the highest imputation accuracies. Therefore, the use of founder breeds in the reference population improves the accuracy of genotype imputation in CA cattle. The results indicate that a multibreed reference population, incorporating founder breeds, could provide a more robust and informative genetic basis for imputing composite cattle.