The Evolution and Role of Molecular Tools in Measuring Diversity and Genomic Selection in Livestock Populations (Traditional and Up-to-Date Insights): A Comprehensive Exploration
by
, ,
Hosameldeen Mohamed Husien
1,2,†
,
Ahmed A. Saleh
3,4,*,†
,
Nada N. A. M. Hassanine
3,4,
Amr M. A. Rashad
4,
Mahmoud A. Sharaby
4,
Asmaa Z. Mohamed
5,
Heba Abdelhalim
6,
Elsayed E. Hafez
7,
Mohamed Osman Abdalrahem Essa
2,8,
Saber Y. Adam
3,
Ning Chen
9,* and
Mengzhi Wang
1,9,* 
1
Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
2
College of Veterinary Medicine, Albutana University, Rufaa 22217, Sudan
3
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
4
Animal and Fish Production Department, Faculty of Agriculture (Al-Shatby), Alexandria University, Alexandria 11865, Egypt
5
Animal and Fish Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt
6
Animal Production Research Institute, Agriculture Research Centre, Giza 12126, Egypt
7
Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria 21934, Egypt
8
College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
9
State Key-Laboratory of Sheep Genetic Improvement and Healthy-Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi 832000, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Vet. Sci. 2024, 11(12), 627; https://doi.org/10.3390/vetsci11120627
Submission received: 27 September 2024
/
Revised: 3 December 2024
/
Accepted: 4 December 2024
/
Published: 6 December 2024
Simple Summary
This investigation highlights the use of advanced molecular tools, especially high-throughput SNP genotyping, in livestock genetic research. These methods identify SNPs, candidate genes, genetic defects, molecular markers, and QTLs, and facilitate whole-genome sequencing (WGS) and genomic selection, which relies on genomic-estimated breeding values (GEBV). Compared to traditional methods, genomic selection enhances breeding decisions, especially for traits that are sex-limited, have low heritability, are measured late, or need reduced generation intervals. The availability of high-density genotyping and next-generation sequencing supports the argument for genome-wide scans for selection. The investigation emphasizes the importance of these technologies in understanding genetic diversity and adaptive selection, identifies candidate genes and QTLs linked to various traits, and underscores advancements in livestock traits like body conformation, meat quality, milk yield, fertility, fiber production, and disease resistance.
Abstract
Distinctive molecular approaches and tools, particularly high-throughput SNP genotyping, have been applied to determine and discover SNPs, potential genes of interest, indicators of evolutionary selection, genetic abnormalities, molecular indicators, and loci associated with quantitative traits (QTLs) in various livestock species. These methods have also been used to obtain whole-genome sequencing (WGS) data, enabling the implementation of genomic selection. Genomic selection allows for selection decisions based on genomic-estimated breeding values (GEBV). The estimation of GEBV relies on the calculation of SNP effects using prediction equations derived from a subset of individuals in the reference population who possess both SNP genotypes and phenotypes for target traits. Compared to traditional methods, modern genomic selection methods offer advantages for sex-limited traits, low heritability traits, late-measured traits, and the potential to increase genetic gain by reducing generation intervals. The current availability of high-density genotyping and next-generation sequencing data allow for genome-wide scans for selection. This investigation provides an overview of the essential role of advanced molecular tools in studying genetic diversity and implementing genomic selection. It also highlights the significance of adaptive selection in light of new high-throughput genomic technologies and the establishment of selective comparisons between different genomes. Moreover, this investigation presents candidate genes and QTLs associated with various traits in different livestock species, such as body conformation, meat production and quality, carcass characteristics and composition, milk yield and composition, fertility, fiber production and characteristics, and disease resistance.
Keywords:
molecular tools; QTLs; NGS; signatures of selection; GWAS; SNP chip; genomic selection
