COWADAPT: Genetic variants for cattle adaptability to harsh environments uncovered through a bovine multi-assembly graph

• Grant number: 24/18544-1
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: April 01, 2025
• End date: November 30, 2025
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Ricardo Vieira Ventura
• Grantee: Thales de Lima Silva
• Supervisor: Hubert Pausch
• Host Institution: Faculdade de Medicina Veterinária e Zootecnia (FMVZ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: Swiss Federal Institute of Technology Zurich, Switzerland
• Associated to the scholarship: 23/06637-2 - COWADAPT: Genetic variants for cattle adaptability to harsh environments uncovered through a bovine multi-assembly graph, BP.PD

Abstract

The extent to which individual indicine cattle genomes contain DNA sequences that are missing in the Hereford-based reference genome is largely unknown. Preliminary analysis in a Brahman assembly, developed by the group of our partner researcher (Animal Genomics ETH), revealed more than 11 million bases (including many putatively novel coding sequences) that were novel when compared to the Hereford-based reference genome. We hypothesize that Nellore cattle carry a similar amount of non-reference bases. In order to make these bases and their variants accessible for genome-wide association analyses planned in work package 4 (WP4) of COWADAPT (WP4: The role of structural variation in cattle adaptation to tropical conditions), we will integrate a referencequality assembly of Nellore into a bovine multi-assembly graph (both of them already developed by Animal Genomics ETH), and build a new multi-assembly graph more representative for indicine cattle. This will enable us to detect Nellorespecific non-reference sequences. In order to make the novel reference bases amenable to population-genomic analyses that rely on a linear reference representation, we will extract all non-reference sequences from the multiassembly graph that originate from the Nellore assembly and append them as additional contigs to the Hereford-based linear reference. This will provide an extended linear reference genome that integrates a well-annotated reference sequence as well as indicine-specific segments that are not included in the standard Bos taurus reference genome. The association between these sequences and traits relevant for the adaptation of Nellore cattle to harsh environments will be tested in WP4.