The Use of Interactive Visualizations for Tracking Haplotypic Inheritance in Livestock

Autor(es)

Selli, Alana ; Miller, Stephen P. ; Ventura, Ricardo V.

• Tipo de documento: Artigo Científico
• Fonte: RUMINANTS; v. 4, n. 1, p. 22-pg., 2024-03-01.

Resumo

Our objective was to harness the power of interactive visualizations by utilizing open-source tools to develop an efficient strategy for visualizing Single Nucleotide Polymorphism data within a livestock population, focusing on tracking the transmission of haplotypes. To achieve this, we simulated a realistic beef cattle population in order to obtain phased haplotypes and generate the necessary inputs for creating our visualizations. The visualization tool was built using Python and the Plotly library, which enables interactivity. We set out to explore three scenarios: trio comparison, visualization of grandparents, and half-sibling evaluation. These scenarios enabled us to trace the inheritance of genetic segments, identify crossover events, and uncover common regions within related and unrelated animals. The potential applications of this approach are significant, particularly for improving genomic selection in smaller breeding programs and farms, and it provides valuable insights for guiding more in-depth genomic region analysis. Beyond its practical applications, we believe this strategy can be a valuable educational tool, helping educators clarify complex concepts like Mendelian sampling and haplotypic diversity. Furthermore, we hope it will encourage livestock producers to adopt advanced technologies like genotyping and genomic selection, thereby contributing to the advancement of livestock genetics. (AU)

• Processo FAPESP: 16/19514-2 - Desenvolvimento de um banco de dados genômicos para a raça Nelore e criação de ferramentas computacionais objetivando a implementação de estudos em larga escala
• Beneficiário: Ricardo Vieira Ventura
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores
• Processo FAPESP: 21/11156-8 - Impactos da inclusão de corridas de homozigosidade em processos de acasalamento dirigido em uma população simulada de bovinos de corte
• Beneficiário: Alana Selli
• Modalidade de apoio: Bolsas no Brasil - Mestrado
• Processo FAPESP: 21/03101-9 - COWADAPT: detecção de variantes genéticas associadas com a adaptação de bovinos a ambientes desafiadores utilizando um multi-assembly graph como referência
• Beneficiário: Ricardo Vieira Ventura
• Modalidade de apoio: Auxílio à Pesquisa - Temático