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.

Revisiting the Velocity Dispersion-Size Relation in Molecular Cloud Structures

Structures in molecular ISM are observed to follow a power-law relation between the velocity dispersion and spatial size,known as Larson’s first relation,which is often attributed to the turbulent nature of molecular ISM and imprints the dynamics of molecular cloud structures.Using the^(13)CO(J=1-0)data from the Milky Way Imaging Scroll Painting survey,we built a sample with 360 structures having relatively accurate distances obtained from either the reddened background stars with Gaia parallaxes or associated maser parallaxes,spanning from 0.4 to~15 kpc.Using this sample and about 0.3 million pixels,we analyzed the correlations between velocity dispersion,surface/column density,and spatial scales.Our structure-wise results show power-law indices smaller than 0.5 in both theσ_(v)-R_(eff)andσ_(v)-R_(eff)·Σrelations.In the pixel-wise results,the v spix is statistically scaling with the beam physical size(R_(s)≡ΘD/2)in form ofσ_(v)^(pix)■R_(s)^(0.43±0.03).Meanwhile,σ_(v)_(pix)in the inner Galaxy is statistically larger than the outer side.We also analyzed correlations betweenσ_(v)_(pix)and the H_(2)column density N(H_(2)),finding thatσ_(v)_(pix)stops increasing with N(H_(2))after>10^(22)cm^(-2).The structures with and without high-column-density(>10^(22)cm^(-2))pixels show differentσ_(v)_(pix)■N(H_(2))^(ξ)relations,where the mean(std)ξvalues are 0.38(0.14)and 0.62(0.27),respectively.

Differentiation potential of bone marrow mesenchymal stem cells in duck

The bone marrow mesenchymal stem cells （MSCs） are multipotent stem cells which can differentiate into mesenchymal cells in vitro. In this study, MSCs in duck were isolated from bone marrow by density gradient centrifuge separation, purified and expanded in the me- dium. The primary MSCs were expanded for 11 passages. The different-passage MSCs were induced to differentiate into osteoblasts and neuron-like cells. Karyotype analysis indicated that MSCs kept diploid condition and the hereditary feature was stable. The different- passage MSCs expressed CD44, ICAM-1 and SSEA-4, but not CD34, CD45 and SSEA-1 when detected by immunofluorescence staining There was no significant difference among the positive rates of passages 2, 6 and 8 （P 〉 0.05）, but a significant difference existed among those of passages 2, 6, 8 and 11 （P 〈 0.05）. After the osteogenic inducement was added, the induced different-passage MSCs expressed high-level alkaline phosphatase （ALP）, and are positive for tetracycline staining, Alizarin Red staining and Von Kossa staining. After the neural inducement was added, about 70% cells exhibited typical neuron-like phenotype, the induced different-passage MSCs expressed Nestin, neuron-specific enolase （NSE） and glial fibrillary acidic protein （GFAP） when detected by immunofluorescence staining. There was no significant difference among the positive rates of passages 3, 4 and 6 （P〉0.05）, but a significant difference existed among those of passages 3, 4, 6 and 8 （P〈0.05）. These results suggest that MSCs in duck were capable of differentiating into osteoblasts and neuron-like cells in vitro.

Whole-genome sequencing identifies functional genes for environmental adaptation in Chinese sheep

Sheep(Ovis aries),among the first domesticated species,are now globally widespread and exhibit remarkable adaptability to diverse environments.In this study,we perform whole-genome sequencing of266 animals from 18 distinct Chinese sheep populations,each displaying unique phenotypes indicative of adaptation to varying environmental conditions.Integrating 131 environmental factors with single nucleotide polymorphism variations,we conduct a comprehensive genetic-environmental association analysis.This analysis identifies 35 key genes likely integral to the environmental adaptation of sheep.The functions of these genes include fat tail formation(HOXA10,HOXA11,JAZF1),wool characteristics(FER,FGF5,MITF,PDE4B),horn phenotypes(RXFP2),reproduction(HIBADH,TRIM71,C6H4orf22),and growth traits(ADGRL3,TRHDE).Notably,we observe a significant correlation between the frequency of missense mutations in the PAPSS2 and RXFP2 genes and variations in altitude.Our study reveals candidate genes for adaptive variation in sheep and demonstrates the diversity in how sheep adapt to their environment.

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.

Metabonomic study of the biochemical profiles of heterozygous myostatin knockout swine

Myostatin is a transforming growth factor-beta family member that normally acts to limit skeletal muscle growth. Myostatin gene (MSTN) knockout (KO) mice show possible effects for the prevention or treatment of metabolic disorders such as obesity and type 2 diabetes. We applied chromatography and mass spectrometry based metabonomics to assess system-wide metabolic response of heterozygous MSTN KO (MSTN+/-) swine. Most of the metabolic data for MSTN+/- swine were similar to the data for wild type (WT) control swine. There were, however, metabolic changes related to fatty acid metabolism, glucose utilization, lipid metabolism, as well as BCAA catabolism caused by monoallelic MSTN depletion. The statistical analyses suggested that: (1) most metabolic changes were not significant in MSTN+/- swine compared to WT swine; (2) only a few metabolic properties were significantly different between KO and WT swine, especially for lipid metabolism. Significantly, these minor changes were most evident in female KO swine and suggested differences in gender sensitivity to myostatin.

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.