Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

BACKGROUND

Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs).

RESULTS

Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms.

CONCLUSIONS

In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Transcriptomic and Metabolomic Analyses Reveal Molecular Regulatory Networks for Pigmentation Deposition in Sheep

Domestic animals have multiple phenotypes of skin and coat color, which arise from different genes and their products, such as proteins and metabolites responsible with melanin deposition. However, the complex regulatory network of melanin synthesis remains to be fully unraveled. Here, the skin and tongue tissues of Liangshan black sheep (black group) and Liangshan semi-fine-wool sheep (pink group) were collected, stained with hematoxylin-eosin (HE) and Masson-Fontana, and the transcriptomic and metabolomic data were further analyzed. We found a large deposit of melanin granules in the epidermis of the black skin and tongue. Transcriptome and metabolome analysis identified 744 differentially expressed genes (DEGs) and 443 differentially expressed metabolites (DEMs) between the pink and black groups. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed the DEGs and DEMs were mainly enriched in the pathways of secondary metabolic processes, melanin biosynthesis processes, melanin metabolism processes, melanosome membranes, pigment granule membranes, melanosome, tyrosine metabolism, and melanogenesis. Notably, we revealed the gene ENSARG00020006042 may be a family member of YWHAs and involved in regulating melanin deposition. Furthermore, several essential genes (TYR, TYRP1, DCT, PMEL, MLANA, SLC45A2) were significantly associated with metabolite prostaglandins and compounds involved in sheep pigmentation. These findings provide new evidence of the strong correlation between prostaglandins and related compounds and key genes that regulate sheep melanin synthesis, furthering our understanding of the regulatory mechanisms and molecular breeding of pigmentation in sheep.

Korean Black Goat Extract Exerts Estrogen-like Osteoprotective Effects by Stimulating Osteoblast Differentiation in MC3T3-E1 Cells and Suppressing Osteoclastogenesis in RAW 264.7 Cells

Postmenopausal osteoporosis, characterized by an imbalance between osteoclast-mediated bone resorption and osteoblast-driven bone formation, presents substantial health implications. In this study, we investigated the role of black goat extract (BGE), derived from a domesticated native Korean goat, estrogen-like activity, and osteoprotective effects in vitro. BGE's mineral and fatty acid compositions were analyzed via the ICP-AES method and gas chromatography-mass spectrometry, respectively. In vitro experiments were conducted using MCF-7 breast cancer cells, MC3T3-E1 osteoblasts, and RAW264.7 osteoclasts. BGE exhibits a favorable amount of mineral and fatty acid content. It displayed antimenopausal activity by stimulating MCF-7 cell proliferation and augmenting estrogen-related gene expression (ERα, ERβ, and pS2). Moreover, BGE positively impacted osteogenesis and mineralization in MC3T3-E1 cells through Wnt/β-catenin pathway modulation, leading to heightened expression of Runt-related transcription factor 2, osteoprotegerin, and collagen type 1. Significantly, BGE effectively suppressed osteoclastogenesis by curtailing osteoclast formation and activity in RAW264.7 cells, concurrently downregulating pivotal signaling molecules, including receptor activator of nuclear factor κ B and tumor necrosis factor receptor-associated factor 6. This study offers a shred of preliminary evidence for the prospective use of BGE as an effective postmenopausal osteoporosis treatment.

A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes

The Anopheles gambiae 1000 Genomes (Ag1000G) Consortium previously utilized deep sequencing methods to catalogue genetic diversity across African An. gambiae populations. We analyzed the complete datasets of 1142 individually sequenced mosquitoes through Microsoft Premonition's Bayesian mixture model based (BMM) metagenomics pipeline. All specimens were confirmed as either An. gambiae sensu stricto (s.s.) or An. coluzzii with a high degree of confidence ( > 98% identity to reference). Homo sapiens DNA was identified in all specimens indicating contamination may have occurred either at the time of specimen collection, preparation and/or sequencing. We found evidence of vertebrate hosts in 162 specimens. 59 specimens contained validated Plasmodium falciparum reads. Human hepatitis B and primate erythroparvovirus-1 viral sequences were identified in fifteen and three mosquito specimens, respectively. 478 of the 1,142 specimens were found to contain bacterial reads and bacteriophage-related contigs were detected in 27 specimens. This analysis demonstrates the capacity of metagenomic approaches to elucidate important vector-host-pathogen interactions of epidemiological significance.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

BACKGROUND

Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures.

RESULTS

We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively.

CONCLUSIONS

In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.

Association between the copy number variation of CCSER1 gene and growth traits in Chinese Capra hircus (goat) populations

Recently, Coiled-coil serine-rich protein 1 (CCSER1) gene is reported to be related to economic traits in livestock, and become a hotspot. In our study, we detected CCSER1 gene CNV in 693 goats from six breeds (GZB, GZW, AN, BH, HG, TH) by quantitative real-time PCR (qPCR) and the association analysis between the types of CNV and growth traits. Then, CCSER1 gene expression pattern was discovered in seven tissues from NB goats. Our results showed that the CCSER1 gene copy numbers were distributed differently in the aforementioned six breeds. The type of CCSER1 gene CNV was significantly associated with body weight and heart girth traits in GZW goat, in which individuals with deletion type were dominant in body weight trait (P < 0.05), while the normal type individuals were more advantageous in heart girth trait (P < 0.01); and there was a significant association with heart girth in TH goat (P < 0.05), which normal type was the dominant one. The expression profile revealed that CCSER1 gene has the highest level in the lung, followed by the small intestine and heart. In conclusion, our result is dedicated to an in-depth study of the novel CCSER1 gene CNV site and to provide essential information for Chinese goats molecular selective breeding in the future.

Coat Color in Local Goats: Influence on Environmental Adaptation and Productivity, and Use as a Selection Criterion

This paper aims to review, systematically synthesize, and analyze fragmented information about the importance of coat color in local goats and its relationship with productivity and other important traits. Topics on current research on color expression are addressed, the relationship that has as a mechanism of environmental adaptation, its relationship with the production of meat, milk, and derivates, and the economic value of this characteristic. The use of this attribute as a tool to establish selection criteria in breeding programs based on results reported in the scientific literature is significant, particularly for low-income production systems, where the implementation of classic genetic improvement schemes is limited due to the lack of productive information, which is distinctive of extensive marginal or low scaled production systems around the world.

A missense mutation in RRM1 contributes to animal tameness

The increased tameness to reduce avoidance of human in wild animals has been long proposed as the key step of animal domestication. The tameness is a complex behavior trait and largely determined by genetic factors. However, the underlying genetic mutations remain vague and how they influence the animal behaviors is yet to be explored. Behavior tests of a wild-domestic hybrid goat population indicate the locus under strongest artificial selection during domestication may exert a huge effect on the flight distance. Within this locus, only one missense mutation RRM1I241V which was present in the early domestic goat ~6500 years ago. Genome editing of RRM1I241V in mice showed increased tameness and sociability and reduced anxiety. These behavioral changes induced by RRM1I241V were modulated by the alternation of activity of glutamatergic synapse and some other synapse-related pathways. This study established a link between RRM1I241V and tameness, demonstrating that the complex behavioral change can be achieved by mutations under strong selection during animal domestication.

Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus)

Artificial and natural selective breeding of goats has resulted in many different goat breeds all around the world. Norduz goat is one of these breeds, and it is a local goat breed of Turkey. The goats are favorable due to pre-weaning viability and reproduction values compared to the regional breeds. Development in sequencing technologies has let to understand huge genomic structures and complex phenotypes. Until now, such a comprehensive study has not been carried out to understand the genomic structure of the Norduz goats, yet. In the study, the next-generation sequencing was carried out to understand the genomic structure of Norduz goat. Real-time PCR was used to evaluate prominent CNVs in the Norduz goat individuals. Whole genome of the goat was constructed with an average of 33.1X coverage level. In the stringent filtering condition, 9,757,980 SNPs, 1,536,715 InDels, and 290 CNVs were detected in the Norduz goat genome. Functional analysis of high-impact SNP variations showed that the classical complement activation biological process was affected significantly in the goat. CNVs in the goat genome were found in genes related to defense against viruses, immune response, and cell membrane transporters. It was shown that GBP2, GBP5, and mammalian ortholog GBP1, which are INF-stimulated GTPases, were found to be high copy numbers in the goats. To conclude, genetic variations mainly in immunological response processes suggest that Norduz goat is an immunologically improved goat breed and natural selection could take an important role in the genetical improvements of the goats.

Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection

BACKGROUND

Short-term, intense artificial selection drives fast phenotypic changes in domestic animals and leaves imprints on their genomes. However, the genetic basis of this selection response is poorly understood. To better address this, we employed the Pekin duck Z2 pure line, in which the breast muscle weight was increased nearly 3-fold after 10 generations of breeding. We denovo assembled a high-quality reference genome of a female Pekin duck of this line (GCA_003850225.1) and identified 8.60 million genetic variants in 119 individuals among 10 generations of the breeding population.

RESULTS

We identified 53 selected regions between the first and tenth generations, and 93.8% of the identified variations were enriched in regulatory and noncoding regions. Integrating the selection signatures and genome-wide association approach, we found that 2 regions covering 0.36 Mb containing UTP25 and FBRSL1 were most likely to contribute to breast muscle weight improvement. The major allele frequencies of these 2 loci increased gradually with each generation following the same trend. Additionally, we found that a copy number variation region containing the entire EXOC4 gene could explain 1.9% of the variance in breast muscle weight, indicating that the nervous system may play a role in economic trait improvement.

CONCLUSIONS

Our study not only provides insights into genomic dynamics under intense artificial selection but also provides resources for genomics-enabled improvements in duck breeding.

Physicochemical Properties of Black Korean Goat Meat with Various Slaughter Ages

This study was conducted to analyze the physicochemical properties of black goat meat according to the slaughter age (3, 6, 9, 12, 24, 36 months). The moisture content tended to decrease, whereas the fat content, pH, and free amino acid composition tended to increase with increasing slaughter age. The collagen content increased significantly with the increasing slaughter age (p < 0.05). The cooking yield showed a tendency to increase up to 12 months of age, and there was no significant difference after 12 months of age. In all mineral contents, the sample for 12 months of age showed higher values than the others. Considering fatty acid composition, the saturated fatty acid content of the 12-month sample had a lower value than the other samples. However, the unsaturated fatty acid of the 12-month sample had higher values than the other samples. Therefore, the best slaughter age for black goats occurs at 12 months of age when nutrition is excellent.

lncRNA-TCONS_00008552 expression in patients with pulmonary arterial hypertension due to congenital heart disease

Long noncoding RNAs (lncRNAs) are potential regulators of a variety of cardiovascular diseases. Therefore, there is a series of differentially expressed lncRNAs in pulmonary arterial hypertension (PAH) that may be used as markers to diagnose PAH and even predict the prognosis. However, their specific mechanisms remain largely unknown. Therefore, we investigated the biological role of lncRNAs in patients with PAH. First, we screened patients with PAH secondary to ventricular septal defect (VSD) and those with VSD without PAH to assess differences in lncRNA and mRNA expression between the two groups. Our results revealed the significant upregulation of 813 lncRNAs and 527 mRNAs and significant downregulation of 541 lncRNAs and 268 mRNAs in patients with PAH. Then, we identified 10 hub genes in a constructed protein-protein interaction network. Next, we performed bioinformatics analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis and subsequently constructed coding-noncoding co-expression networks. We screened lncRNA-TCONS_00008552 and lncRNA-ENST00000433673 as candidate genes and verified the expression levels of the lncRNAs using quantitative reverse-transcription PCR. Although expression levels of lncRNA-TCONS_00008552 in the plasma from the PAH groups were significantly increased compared with the control groups, there was no significant difference in the expression of lncRNA-ENST00000433673 between the two groups. This study bolsters our understanding of the role of lncRNA in PAH occurrence and development and indicates that lncRNA-TCONS_00008552 is a novel potential molecular marker for PAH.

Identification of selection signatures in Capra hircus and Capra aegagrus in Iran

Identification of selection signatures may provide a better understanding of domestication process and candidate genes contributing to this process. In this study, two populations of domestic and wild goats from Iran were analyzed to identify selection signatures. RSB, iHS, and XP-EHH statistics were used in order to identify robust selection signatures in the goat genome. Genotype data of domestic and wild goats from the NextGen project was used. The data was related to 18 Capra aegagrus (wild goat) and 20 Capra hircus (domestic goat) from Iran. The iHS method indicated 675 and 441 selection signatures in C. aegagrus and C. hircus, respectively. RSB and XP-EHH methods showed about 370 and 447 selection signatures in C. aegagrus and C. hircus, respectively. These selection signatures were mainly associated with milk production, fleece trait, mammary epithelial cells, reproduction, and immune system.

Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats (Capra hircus)

Simple Summary

During the present decade, highly selected caprine farming has increased in popularity due to the hardiness and adaptability inherent to goats. Recent advances in genetics have enabled the improvement in goat selection efficiency. The present review explores how genetic technologies have been applied to the goat-farming sector in the last century. The main candidate genes related to economically relevant traits are reported. The major source of income in goat farming derives from the sale of milk and meat. Consequently, yield and quality must be specially considered. Meat-related traits were evaluated considering three functional groups (weight gain, carcass quality and fat profile). Milk traits were assessed in three additional functional groups (milk production, protein and fat content).

Abstract

Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in genomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability.

Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection

Background

The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands.

Results

Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed-specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures.

Conclusions

We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00695-w.

CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly

Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.

Characteristics of the Allele Pool and the Genetic Differentiation of Goats of Different Breeds and their Wild Relatives by Str-Markers

Based on 16 STR-loci, the allele pool and interbreed differentiation of goat breeds of Russian and foreign breeding were investigated in this study. These breeds included Karachai (KRCH-K, n=73, mountain zone; KRCH-Z, n=33, foothill zone), Dagestan Downy (DAGD, n=30), Dagestan Wool (DAGW, n=30), Soviet Wool (SOVW, n=30), Saanen (SAAN, n=34), Murciano-Granadina (MURS, n=37), as well as wild goats, represented by three species of mountain goats (n=52): Siberian Capricorn (Capra sibirica) of Altai (CSIB-S, n=6), Tajikistan (CSIB-T, n=4), Kyrgyzstan (CSIB-K, n=6), and the Himalayas (CSIB-H, n=4); Bezoar goat (Capa aegagrus) of Turkey (CAEG, n=3) and Pakistan (CAEG-S, n=3); West Caucasian tur (Capra caucasica): western Caucasian (Kuban, CCAU-K, n=10), central Caucasian (CCAU-M, n=8), and eastern Caucasian (Dagestan, CCAU-D, n=8). The highest genetic diversity was observed in the North Caucasus breeds, such as Karachai, Dagestan Downy, and Dagestan Wool. The mean numbers of alleles per locus and allelic diversity were 7.385-9.154 and 7.353-7.713, respectively. The genetic proximity of Caucasian breeds was confirmed by cluster analysis, and they formed a common branch with the highest genetic affinity, while the Orenburg and Soviet Wool breeds formed another branch, and the third branch with the least affinity was the dairy breed of foreign selection.The analysis of the phylogenetic tree of domestic and wild species established the formation of three clusters formed by the subspecies of the West Caucasian tur, Siberian ibex, and breeds of domestic goats. At the same time, populations of the Bezoar goats were localized at the root of the last cluster, which confirmed their role as the ancestors of domestic goats.

Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats

The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (F_ST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.

Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex

The Nubian ibex (Capra nubiana) is a wild goat species that inhabits the Sahara and Arabian deserts and is adapted to extreme ambient temperatures, intense solar radiation, and scarcity of food and water resources. To investigate desert adaptation, we explored the possible role of copy number variations (CNVs) in the evolution of Capra species with a specific focus on the environment of Capra nubiana. CNVs are structural genomic variations that have been implicated in phenotypic differences between species and could play a role in species adaptation. CNVs were inferred from Capra nubiana sequence data relative to the domestic goat reference genome using read-depth approach. We identified 191 CNVs overlapping with protein-coding genes mainly involved in biological processes such as innate immune response, xenobiotic metabolisms, and energy metabolisms. We found copy number variable genes involved in defense response to viral infections (Cluster of Differentiation 48, UL16 binding protein 3, Natural Killer Group 2D ligand 1-like, and Interferon-induced transmembrane protein 3), possibly suggesting their roles in Nubian ibex adaptations to viral infections. Additionally, we found copy number variable xenobiotic metabolism genes (carboxylesterase 1, Cytochrome P450 2D6, Glutathione S-transferase Mu 4, and UDP Glucuronosyltransferase-2B7), which are probably an adaptation of Nubian ibex to desert diets that are rich in plant secondary metabolites. Collectively, this study's results advance our understanding of CNVs and their possible roles in the adaptation of Nubian ibex to its environment. The copy number variable genes identified in Nubian ibex could be considered as subjects for further functional characterizations.

Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation

Pashmina goats produce the world's finest and the most costly animal fiber (Pashmina) with an average fineness of 11-13 microns and have more evolved mechanisms than any known goat breed around the globe. Despite the repute of Pashmina goat for producing the finest and most sought-after animal fiber, meager information is available in the public domain about Pashmina genomics and transcriptomics. Here we present a 2.94 GB genome sequence from a male Changthangi white Pashmina goat. We generated 294.8 GB (>100X coverage) of the whole-genome sequence using the Illumina HiSeq 2500 sequencer. All cleaned reads were mapped to the goat reference genome (2,922,813,246 bp) which covers 97.84% of the genome. The Unaligned reads were used for de novo assembly resulting in a total of 882 MB non-reference contigs. De novo assembly analysis presented in this study provides important insight into the adaptation of Pashmina goats to cold stress and helps enhance our understanding of this complex phenomenon. A comparison of the Pashmina goat genome with a wild goat genome revealed a total of 2,823 high impact single nucleotide variations and small insertions and deletions, which may be associated with the evolution of Pashmina goats. The Pashmina goat genome sequence provided in this study may improve our understanding of complex traits found in Pashmina goats, such as annual fiber cycling, defense mechanism against hypoxic, survival secret in extremely cold conditions, and adaptation to a sparse diet. In addition, the genes identified from de novo assembly could be utilized in differentiating Pashmina fiber from other fibers to avoid falsification at marketing practices.

The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat

The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.

Genomics of Adaptations in Ungulates

Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.

Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Simple Summary

In the local populations, the increase in inbreeding is a relevant problem for the reduction in production, reproduction, and adaptive traits. The application of genomic technologies has facilitated the assessment of inbreeding in these populations. The current study aims to investigate the patterns of homozygosity in five Italian local goat populations. The results showed the different selection histories and breeding schemes of these goat populations. The analysis also indicated the importance of this information to avoid future loss of diversity and to produce information for designing optimal breeding and conservation programs.

Abstract

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

Capturing the Effects of Domestication on Vocal Learning Complexity

Domesticated and vocal learning species can serve as informative model organisms for the reduction of reactive aggression and emergence of speech in our lineage. Amidst mounting evidence that domestication modifies vocal repertoires across different species, we focus on the domesticated Bengalese finch, which has a more complex song than the wild-type white-rumped munia. Our explanation for this effect revolves around the glutamate neurotransmitter system. Glutamate signaling (i) is implicated in birdsong learning, (ii) controls dopamine activity in neural circuits crucial for vocal learning, (iii) is disproportionately targeted in the evolution of domesticates, and (iv) regulates stress responses and aggressive behaviors attenuated under domestication. We propose that attenuated excitation of stress-related neural circuits potentiates vocal learning via altered dopaminergic signaling.

GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions

Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data. With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples, a user-friendly database making efficient reuse of these important resources is needed. Here, we use the genomes of 208 modern domestic goats, 24 bezoars, 46 wild ibexes, and 82 ancient goats to present a comprehensive goat genome variation database (GGVD). GGVD hosts a total of ∼41.44 million SNPs, ∼5.14 million indels, 6,193 selected loci, and 112 introgression regions. Users can freely visualize the frequency of genomic variations in geographical maps, selective sweeps in interactive tables, Manhattan plots, or line charts, as well as the heatmap patterns of the SNP genotype. Ancient data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early, middle, and late stages. For facilitating access to sequence features, the UCSC Genome Browser, BLAT, BLAST, LiftOver, and pcadapt are also integrated into GGVD. GGVD will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs, and it is publicly available at http://animal.nwsuaf.edu.cn/GoatVar.

An atlas of CNV maps in cattle, goat and sheep

Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study (GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected (P<0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms (SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.

Genetic Mapping of Climbing and Mimicry: Two Behavioral Traits Degraded During Silkworm Domestication

Behavioral changes caused by domestication in animals are an important issue in evolutionary biology. The silkworm, Bombyx mori, is an ideal fully domesticated insect model for studying both convergent domestication and behavior evolution. We explored the genetic basis of climbing for foraging and mimicry, two degraded behaviors during silkworm domestication, in combination of bulked segregant analysis (BSA) and selection sweep screening. One candidate gene, ASNA1, located in the 3-5 Mb on chromosome 19, harboring a specific non-synonymous mutation in domestic silkworm, might be involved in climbing ability. This mutation was under positive selection in Lepidoptera, strongly suggesting its potential function in silkworm domestication. Nine candidate domesticated genes related to mimicry were identified on chromosomes 13, 21, and 27. Most of the candidate domesticated genes were generally expressed at higher levels in the brain of the wild silkworm. This study provides valuable information for deciphering the molecular basis of behavioral changes associated with silkworm domestication.

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

Background

Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) to public data for 26 individuals from three other breeds (two Moroccan and one Chinese) and 21samples from Bezoar ibexes.

Results

We obtained a total of 2394 CNV regions (CNVRs) by merging 208,649 high-confidence CNVs, which spanned ~ 267 Mb of total length and accounted for 10.80% of the goat autosomal genome. Functional analyses showed that 2322 genes overlapping with the CNVRs were significantly enriched in 57 functional GO terms and KEGG pathways, most related to the nervous system, metabolic process, and reproduction system. Clustering patterns of all 85 samples generated separately from duplications and deletions were generally consistent with the results from SNPs, agreeing with the geographical origins of these goats. Based on genome-wide F_ST at each CNV locus, some genes overlapping with the highly divergent CNVs between domestic and wild goats were mainly enriched for several immunity-related pathways, whereas the genes overlapping with the highly differentiated CNVs between highland and lowland goats were mainly related to vitamin and lipid metabolism. Remarkably, a 507-bp deletion at ~ 14 kb downstream of FGF5 on chromosome 6 showed highly divergent (F_ST = 0.973) between the highland and lowland goats. Together with an enhancer activity of this sequence shown previously, the function of this duplication in regulating fiber growth deserved to be further investigated in detail.

Conclusion

We generated a comprehensive map of CNVs in goats. Many genetically differentiated CNVs among various goat populations might be associated with the population characteristics of domestic goat breeds.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07267-6.

Gaze Following in Ungulates: Domesticated and Non-domesticated Species Follow the Gaze of Both Humans and Conspecifics in an Experimental Context

Gaze following is the ability to use others' gaze to obtain information about the environment (e.g., food location, predators, and social interactions). As such, it may be highly adaptive in a variety of socio-ecological contexts, and thus be widespread across animal taxa. To date, gaze following has been mostly studied in primates, and partially in birds, but little is known on the gaze following abilities of other taxa and, especially, on the evolutionary pressures that led to their emergence. In this study, we used an experimental approach to test gaze following skills in a still understudied taxon, ungulates. Across four species (i.e., domestic goats and lamas, and non-domestic guanacos and mouflons), we assessed the individual ability to spontaneously follow the gaze of both conspecifics and human experimenters in different conditions. In line with our predictions, species followed the model's gaze both with human and conspecific models, but more likely with the latter. Except for guanacos, all species showed gaze following significantly more in the experimental conditions (than in the control ones). Despite the relative low number of study subjects, our study provides the first experimental evidence of gaze following skills in non-domesticated ungulates, and contributes to understanding how gaze following skills are distributed in another taxon-an essential endeavor to identify the evolutionary pressures leading to the emergence of gaze following skills across taxa.

Detection of Selection Signatures Underlying Production and Adaptive Traits Based on Whole-Genome Sequencing of Six Donkey Populations

Simple Summary

After a long period of artificial selection, the donkey now presents a variety of body types and production performance values. In this experiment, we performed selective signal scanning on the second-generation resequencing data of six different varieties. The regions and candidate genes related to artificial selection were identified to provide reference for future breeding.

Abstract

Donkeys (Equus asinus) are an important farm animal. After long-term natural and artificial selection, donkeys now exhibit a variety of body sizes and production performance values. In this study, six donkey breeds, representing different regions and phenotypes, were used for second-generation resequencing. The sequencing results revealed more than seven million single nucleotide variants (SNVs), with an average of more than four million SNVs per species. We combined two methods, Z-transformed heterozygosity (ZHp) and unbiased estimates of pairwise fixation index (di) values, to analyze the signatures of selection. We mapped 11 selected regions and identified genes associated with coat color, body size, motion capacity, and high-altitude adaptation. These candidate genes included staining (ASIP and KITLG), body type (ACSL4, BCOR, CDKL5, LCOR, NCAPG, and TBX3), exercise (GABPA), and adaptation to low-oxygen environments (GLDC and HBB). We also analyzed the SNVs of the breed-specific genes for their potential functions and found that there are three varieties in the conserved regions with breed-specific mutation sites. Our results provide data to support the establishment of the donkey SNV chip and reference information for the utilization of the genetic resources of Chinese domestic donkeys.

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

A genome-wide analysis of copy number variation in Murciano-Granadina goats

BACKGROUND

In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions.

RESULTS

Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10^-10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10^-04) and bile secretion (fold-enrichment = 3.90, q-value = 5.70 × 10^-03).

CONCLUSIONS

A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination.

Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China

Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.

Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations

Simple Summary

Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes and are known to be present in genomic regions that regulate important physiological functions. In this study, CNV detection was performed starting from genotypic data of 120 individuals, belonging to four Sicilian dairy goat breeds, genotyped with the Illumina GoatSNP50 BeadChip array. Using PennCNV software, a total of 702 CNVs were identified in 107 individuals. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair. Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs, which are involved in local adaptation, mild behaviour, immune response, reproduction, and olfactory receptors. This study provides insights into the genomic variations within these Italian goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.

Abstract

Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.

The origin of domestication genes in goats

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanisms of animal domestication.

Genomic insights into ruminant evolution: from past to future prospects

Ruminants (Ruminantia) are among the most successful herbivorous mammals, exhibiting wide-ranging morphological and ecological characteristics (such as headgear and multichambered stomach) and including various key livestock species (e.g., cattle, buffalo, yak, sheep, and goat). Understanding their evolution is of great significance not only in scientific research but also in applications potential for human society. The rapid growth of genomic resources provides unprecedented opportunities to dissect the evolutionary histories and molecular mechanisms underlying the distinct characteristics of ruminants. Here we summarize our current understanding of the genetic, morphological, and ecological diversity of ruminants and provide prospects for future studies.

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome

It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock. However, the rich diversity of worldwide goat breeds indicates that a genome from one individual would be insufficient to represent the whole genomic contents of goats. By comparing nine de novo assemblies from seven sibling species of domestic goat with ARS1 and using resequencing and transcriptome data from goats for verification, we identified a total of 38.3 Mb sequences that were absent in ARS1. The pan-sequences contain genic fractions with considerable expression. Using the pan-genome (ARS1 together with the pan-sequences) as a reference genome, variation calling efficacy can be appreciably improved. A total of 56,657 spurious SNPs per individual were repressed and 24,414 novel SNPs per individual on average were recovered as a result of better reads mapping quality. The transcriptomic mapping rate was also increased by ∼1.15%. Our study demonstrated that comparing de novo assemblies from closely related species is an efficient and reliable strategy for finding missing sequences from the reference genome and could be applicable to other species. Pan-genome can serve as an improved reference genome in animals for a better exploration of the underlying genomic variations and could increase the probability of finding genotype-phenotype associations assessed by a comprehensive variation database containing much more differences between individuals. We have constructed a goat pan-genome web interface for data visualization (http://animal.nwsuaf.edu.cn/panGoat).

Skin transcriptome profiles associated with black- and white-coated regions in Boer and Macheng black crossbred goats

To increase the current understanding of the gene-expression profiles in different skin regions associated with different coat colors and identify key genes for the regulation of color patterns in goats, we used the Illumina RNA-Seq method to compare the skin transcriptomes of the black- and white-coated regions containing hair follicles from the Boer and Macheng Black crossbred goat, which has a black head and a white body. Six cDNA libraries derived from skin samples of the white-coated region (n = 3) and black-coated region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for skin samples from black- and white-coated regions, respectively, of which 75.39% and 76.05% were covered in the genome database. A total of 165 differentially expressed genes (DEGs) were detected between these two color regions, among which 110 were upregulated and 55 were downregulated in the skin samples of white- vs. black-coated regions. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of these DEGs may play an important role in controlling the pigmentation of skin or hair follicles. We identified three key DEGs, i.e., Agouti, DCT, and TYRP1, in the pathway related to melanogenesis in the different skin regions of the crossbred goat. DCT and TYRP1 were downregulated and Agouti was upregulated in the skin of the white-coated region, suggesting a lack of mature melanocytes in this region and that Agouti might play a key developmental role in color-pattern formation. All data sets (Gene Expression Omnibus) are available via public repositories. In addition, MC1R was genotyped in 200 crossbred goats with a black head and neck. Loss-of-function mutations in MC1R as well as homozygosity for the mutant alleles were widely found in this population. The MC1R gene did not seem to play a major role in determining the black head and neck in our crossbred goats. Our study provides insights into the transcriptional regulation of two distinct coat colors, which might serve as a key resource for understanding coat color pigmentation in goats. The region-specific expression of Agouti may be associated with the distribution of pigments across the body in Boer and Macheng Black crossbred goats.

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case-control genome-wide association study (GWAS), the Bayesian population differentiation analysis (F_ST ) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and F_ST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and F_ST analyses. Moreover, one candidate marker identified by GWAS and F_ST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome-wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome-wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations.

Characterization of lncRNA-miRNA-mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle

There is growing evidence that non-coding RNAs are emerging as critical regulators of skeletal muscle development. In order to reveal their functional roles and regulatory mechanisms, we constructed a lncRNA–miRNA–mRNA network according to the ceRNA (competitive endogenous RNA) theory, using our high-throughput sequencing data. Subsequently, the network analysis, GO (Gene Ontology) analysis, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed for functional annotation and exploration of lncRNA ceRNAs. The results uncovered a scale-free characteristics network which exhibited high functional specificity for bovine skeletal muscle development: co-expression lncRNAs were significantly enriched in muscle development related biological processes and the Wnt signaling pathway. Furthermore, GSEA (Gene Set Enrichment Analysis) indicated that the risk score has a tendency to associate with myogenesis, and differentially expressed RNAs were validated by qPCR, further confirming the credibility of our network. In summary, this study provides insights into lncRNA-mediated ceRNA function and mechanisms in bovine skeletal muscle development and will expand our understanding of lncRNA biology in mammals.

New world goat populations are a genetically diverse reservoir for future use

Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.

Decrease of gene expression diversity during domestication of animals and plants

BACKGROUND

The genetic mechanisms underlying the domestication of animals and plants have been of great interest to biologists since Darwin. To date, little is known about the global pattern of gene expression changes during domestication.

RESULTS

We generated and collected transcriptome data for seven pairs of domestic animals and plants including dog, silkworm, chicken, rice, cotton, soybean and maize and their wild progenitors and compared the expression profiles between the domestic and wild species. Intriguingly, although the number of expressed genes varied little, the domestic species generally exhibited lower gene expression diversity than did the wild species, and this lower diversity was observed for both domestic plants and different kinds of domestic animals including insect, bird and mammal in the whole-genome gene set (WGGS), candidate selected gene set (CSGS) and non-CSGS, with CSGS exhibiting a higher degree of decreased expression diversity. Moreover, different from previous reports which found 2 to 4% of genes were selected by human, we identified 6892 candidate selected genes accounting for 7.57% of the whole-genome genes in rice and revealed that fewer than 8% of the whole-genome genes had been affected by domestication.

CONCLUSIONS

Our results showed that domestication affected the pattern of variation in gene expression throughout the genome and generally decreased the expression diversity across species, and this decrease may have been associated with decreased genetic diversity. This pattern might have profound effects on the phenotypic and physiological changes of domestic animals and plants and provide insights into the genetic mechanisms at the transcriptome level other than decreased genetic diversity and increased linkage disequilibrium underpinning artificial selection.

Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation

After domestication 11 000 years ago in Asia Minor, the goat followed human migration to Europe and Asia. It was then introduced in Africa and is now raised all over the world. In this study, we exploited a dataset composed of 54 000 SNPs (Illumina goat DNA chip) to analyze the genetic diversity of 223 individuals belonging to eight French breeds (Alpine, Angora, Corse, Fossés, Poitevine, Provençale, Pyrénées and Saanen). Analyses carried out included individual-based approaches (principal component analysis and population structure) and population-based approaches (phylogenetic tree constructions). The results of the genetic diversity analyses revealed that French breeds are clearly differentiated, in particular, the Angora breed that originates from south west Asia. The Provençale breed shows a very original genetic pattern that could be the result of ancient admixture. Then, selection signatures were detected by identifying regions of outlying genetic differentiation between populations. Five genomic regions were detected under selection on chromosomes 5, 6, 11, 13 and 20, revealing mainly soft selective sweeps and a few hard selective sweeps and highlighting candidate genes that had been selected for during the evolutionary history of these breeds. Among them, two coat coloration genes (ADAMTS20 and ASIP) and one gene related to milk composition (CSN1S1) were involved.