Next Generation Sequencing Technologies and Their Applications in Livestock Genomics: A Comprehensive Review
DOI:
https://doi.org/10.14741/ijab/v.9.1.1Keywords:
Next generation sequencing, Whole genome sequencing, RNA- seq, Livestock genomics, 1000 Bull Genomes, Rumen metagenomics, Transcriptomics, Epigenomics, Reference genome assembly, BioinformaticsAbstract
Next- generation sequencing (NGS) technologies have transformed the scope, speed, and economics of livestock genomics research, enabling comprehensive characterisation of genetic variation, transcriptome dynamics, epigenomic landscapes, and gut and rumen microbial communities with a thoroughness that was inconceivable in the pre- NGS era. Since the commercialisation of massively parallel sequencing platforms in 2007-2008 and the subsequent completion of chromosome level reference genome assemblies for cattle, pig, sheep, goat, horse, and chicken using both short- read and long- read sequencing, NGS has progressively transitioned from a purely research tool to an operational component of genomic selection, veterinary diagnostics, and livestock population genomics. This comprehensive review examines the principal NGS platforms — Illumina (HiSeq X, NovaSeq 6000), Pacific Biosciences (Sequel II), Oxford Nanopore Technologies (MinION, PromethION), and BGI DNBseq — comparing their strengths, limitations, and applications in livestock. The major application domains covered include whole- genome sequencing (WGS) for variant discovery and imputation panel construction, RNA- seq for transcriptomics of economically important tissues and physiological states, ChIP- seq and ATAC- seq for epigenomic annotation, rumen and gut metagenomics for microbiome characterisation, single- cell sequencing for developmental biology, and long- read sequencing for chromosome- scale reference genome assembly. The 1000 Bull Genomes Project is examined as the model international consortium for NGS- based livestock population sequencing. Bioinformatics pipelines, quality control standards, and data management challenges are reviewed. The review concludes with a perspective on the convergence of NGS with CRISPR genome editing, precision livestock farming, and artificial intelligence that is defining the frontier of livestock genomics as of 2019.
