Genomics And Community-Based Breeding Programs To Enhance Breeding of Goats And Sheep In Uganda

Introduction

• Adaptation of ruminants (cattle, goats and sheep) to a number of environment changes and stresses is a combination of physiological, morphological, behavioral and genetic mechanisms.
• The environmental stresses mainly include: heat stress, high altitude, lowlands, nutritional stress etc. The information provided below shows the genetic adaptability measures whereby different literature sources have been reviewed to identify some of the genes/candidate genes and their function.

Objectives

1. Study the Geographical distribution and Population structure of Goats, Sheep and Cattle.
2. Genome-Wide Analysis of Traits governing environmental adaptation among Goats, sheep and cattle.
3. Characterization of Genetic Variations in Goat, Sheep and Cattle responsible for adaptation to different environments.

Project Activities:

• Develop goat genome sequence as a research tool/resource
• Developing tools to characterize breed structure and geographic distribution in caprina genome
• Develop genotype/phenotype programs for selective breeding
• Identify teams and methods for implementing breeding
• Develop a short policy paper that will guide the planning and implementation of the objectives of this research group
• Collaborate with specialized groups such as International Goat Genome Consortium to develop genomic breeding tools.
• Use community-based breeding programs to enhance breeding.

Identification of genes responsible for environmental adaptation among the three species

• Whole-genome sequences from domesticated cattle, sheep and goats retrieved from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra:).
• All genome raw data in NCBI SRA format will be retrieved and converted into the fastq format using the fastq-dump 2.8.2 tool available in the SRA toolkits package (https://www.ncbi.nlm.nih.gov/sra/ docs/toolkitsoft/).

Phylogenetic Analysis

• Phylogeny being an essential biological tool that reflects the evolutionary history of different species or lineages and divergent events, helps in tracing evolution of distinct complex characteristic amongst species. A phylogenetic tree will be created using Muscle results from FASTA files downloaded for each gene responsible for the trait under study.
• The phylogenetic tree and percent similarity matrix will be constructed using all identified genes for different environment adaptation traits previously annotated for sheep (Baylor College of Medicine Human Genome Sequencing Center), cattle (USDAARS), and goat (USDAARS).

Discovery and comparison of Genomic Variations among three species:

• Fastq files will be filtered using Trimom-matic software (version 0.36, Bolger et al., 2014) with an aim of obtaining high-quality SNP and insertion/deletions (INDEL). After filtering, only paired-end reads will be used in the next step of alignment whereby sequences will be aligned to reference genome.
• All the files in sequence alignment map (SAM) format will be sorted and converted into binary format in order to get rid of PCR duplicates and to realign INDEL regions with the Picard tool (https://broadinstitute.github.io/picard/). We will use the HaplotypeCaller function of the Genome Analysis Toolkit (GATK, version 3.8) to generate vcf (variant call format) files.

Environment adaptation traits among goats, sheep and cattle:

Bibliometrics analysis will be performed on the data obtained from the WoS Core Collection database for publications and citations. The process of data exportation from citations to InCites database will be done for analysis of different environment adaptation traits studied recently by

different researchers. The WoS Core Collection database will be used to search all publications around the globe but major focus will be on papers in line to environmental adaptation among small ruminants (goats, cattle and sheep) since our study focused scientific well documented research outputs.