A review of the pangenome:how it affects our understanding of genomic variation,selection and breeding in domestic animals?

As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

Whole-genome sequencing reveals selection signals among Chinese,Pakistani,and Nepalese goats

The goat(Capra hircus)is one of the oldest domesticated animal species,with archeological evidence indicating that its earliest domestication from the wild ancestor(bezoar)occurred in the Fertile Crescent 10,000 calibrated calendar years ago(Zeder and Hesse,2000).A variety of well-adapted goat breeds with excellent economic traits have been selected artificially and naturally for human needs in China,Pakistan,and Nepal.For example,cashmere goat breeds produce fine cashmere wool and are mainly distributed on the Himalayan Plateau(e.g.,Nepal and Tibet)and in cold northern China(e.g.,Inner Mongolia and Liaoning).The Toggenburg dairy goat is the most productive breed of dairy goat and is distributed in at least 50 countries on all continents(Ferro et al.,2017).Pakistani ewes are reared mostly for meat and wool purposes,but some are used as dairy goats,such as the Bugi Toori goat and Pateri goat(Bilal et al.,2018).Additionally,indigenous goats of the southern Asian regions are well adapted to the local hot environment.Their unique traits and biodiversity serve as genetic resources that can be used for the artificial breeding of goats.Recently,several studies have provided patterns of genome-wide characteristics in goat populations to explore the underlying genetic basis of trait formation and environmental adaptability in China(Zhang et al.,2018),Pakistan(Kumar et al.,2018),and Nepal(Sasazaki et al.,2021),respectively.However,due to the proximity of these geographic regions,the profiles of genetic differences,gene flow,and common genes related to high trait performance between goat populations from China,Pakistan,and Nepal remain unclear.

Genomic regions under selection for important traits in domestic horse breeds

Horses were domesticated 5500 years ago,thousands of years later than other domestic animals;however, in this relatively short period, domestic horses have had a great impact on human history by accelerating civilization, revolutionizing warfare and advancing agricultural production. Modern breeding using markerassisted selection has greatly accelerated breeding progress. Therefore, identification of genetic markers underlying the traits of interest in domestic horses is the basis for the modern breeding system. In this review, we present an overview of genetic mapping studies and genome wide analyses to identify the genomic regions targeted by positive selection for four important aspects of horses, coat color, racing performance, gait and height at withers. The MC1 R locus, for example, has been shown to be the main gene responsible for chestnut color, and the MSTN locus has been shown to control the muscle fiber growth in racing breeds. The missense mutation in DMRT3 is the causal mutation for the alternate gaits in horses. Height at withers, a quantitative trait, was mapped to four major loci(3:105547002, 6:81481064, 9:75550059 and 11:23259732) that can explain 83% of the height variations in domestic horses.