RGD v2.0: a major update of the ruminant functional and evolutionary genomics database.

Ruminant Genome Database (RGD; http://animal.nwsuaf.edu.cn/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; ∼8 600 000 conserved elements; and ∼1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.

Performance of Black Bengal goat: a 50-year review.

Black Bengal goat (BBG) is the most widely recognized legacy goat breed in Bangladesh. The breed is black in color yet likewise earthy, white, or dim colors additionally found. The breed has medium body size with grown-up weight 25-30 kg, little horns, short legs, and tight body structure. The BBG is one of the most compliant, all around adjusted, early maturing, prolific, productive, and tropical disease-resistant goat types of the world that produces incredible quality meat, milk, and skin. The breed is versatile in hot, moist, cruel, climatic conditions and flourishes well on a cacophonous dietary regimen from uncultivable decrepit grounds, residences, riversides, banks, sloping, and hilly territories where crop culture or dairy nourishing is inconceivable. In Bangladesh, the BBG is one of the main red meat-producing small ruminants which shares remarkable local interest during Eid-Ul-Adha, Eid-Ul-Fitr, wedding ceremony, birthday festival, circumcision, memorial programs, and other social celebrations with no social, cultural, and religious limitations. Being little in size, the BBG has been an amazing asset to advance supportable vocations for the negligible, little, and landless ranchers who rely upon free regular grazing lands for raising domesticated animals. Regardless of incredibly exceptional components and features, the production of BBG has not yet been popularized widely since meager consideration has been paid for improving their efficiency. Development of cutting edge hereditary, dietary, and health as well as disease control procedure and utilization of modern management frameworks may procure considerable changes in improving the overall performance of the BBG.

Evaluation of morphological traits and physiological variables of several Chinese goat breeds and their crosses.

The current study was undertaken to evaluate some morphological traits of the goat breeds raised in Southwest China. The field experimentation and data collection were from 434 animals presenting seven breeds of the Dazu black goat (DBG; n = 203), Saanen milk goat (SMG; n = 50), Black Boer × Dazu black goat (BXC; n = 28), Hechuan white goat (HWG; n = 49), Inner Mongolia Cashmere goat (IMCG; n = 25), IMCG × DBG (F1; n = 57) and F1 × F1 (F2; n = 22). All studied animals were adult and selected to be at the same age (36.50 ± 0.75 months). After editing, more than 20 morphological and production traits like body condition score (BCS), testicle measurements, coat colour, fibre traits, skin colour, horn colour, horn shape, horn orientation, wattles, front hair, beard, ear shape, ear size, rump angle, hind leg angulation and physiological variables were analysed. BXC and DBG had dark coat colour, whilst SMG, HWG and IMCG had light colour, whilst F1 and F2 ranged from light to dark coat colour. Concerning BCS, the breeds BXC and DBG were characterized as fat goats, whilst SMG, HWG, F1 and F2 were average, whilst IMCG was thin. The maximum values for testis measurements were recorded for BXC, SMG and DBG. For fibre traits, IMCG, F1 and F2 were the most superior. BXC and DBG males have good fertility parameters. The highest values for rectal temperature, skin temperature and breath rate were recorded for SMG. These findings revealed the presence of a wide range of morphological differences among studied goat breeds. Such diversity in the performance of goat breeds raised in Southwest China is crucial to implement reliable selection strategies for breeding goats in this area.

Whole-genome resequencing reveals diversity and selective signals in Longlin goat.

The Longlin goat is one of the most valuable livestock species in Guangxi Autonomous Region of China, but its genomic diversity and selective signals are not clearly elucidated. Here we compared 20 genomes of Longlin goat to 66 genomes of other seven goat breeds worldwide to analyze patterns of Longlin goat genetic variation. We found the lowest linkage disequilibrium at the large distances between SNPs associated with the highest effective population size in the recent generations ago in Longlin goat. The eight goat breeds could be divided into Euro-African and East Asian goat population. Interestingly, like East Asian taurine, the same two migration phases might have occurred in the history of East Asian goat. More importantly, we identified selective signals implicated in immune resistance to disease, especially for skin disease, in Longlin goat. Our findings will not only help understand the evolutionary history and breed characteristic but can provide valuable resources for conservation of germplasm resources and implementation of crossbreeding programs.

A highly selective two-way purification method using liquid chromatography for isolating αS2-casein from goat milk of five different breeds.

The main challenges in the purification of αS2-casein are due to the low quantity in milk and high homology with other casein subunits, i.e., αS1-casein, ß-casein, and κ-casein. To overcome these challenges, the aim of this study was to develop a two-step purification to isolate native αS2-casein in goat milk from five different breeds; British Alpine, Jamnapari, Saanen, Shami, and Toggenburg. The first step of the purification was executed by anion-exchange chromatography under optimal elution conditions followed by size exclusion chromatography. Tryptic peptides from in-gel digestion of purified αS2-casein were sequenced and analyzed by LC-ESI-MS/MS. From 1.05 g of whole casein, the highest yield of αS2-casein (6.7 mg/mL) was obtained from Jamnapari and the lowest yield (2.2 mg/mL) was from Saanen. A single band of pure αS2-casein was observed on SDS-PAGE for all breeds. The αS2-casein showed coverage percentage of amino acid sequence from 76.68 to 92.83%. The two-step purification process developed herein was successfully applied for isolating native αS2-casein from goat milk with high purity, which will allow for future in vitro studies to be conducted on this protein.

The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species.

BACKGROUND: Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse environmental conditions. Despite the relevance of this species, the genetic research on the goat traits is limited compared to other domestic species. Thanks to the latest goat reference genomic sequence (ARS1), which is considered to be one of the most continuous assemblies in livestock, we deduced the genomic structure of the T cell receptor beta (TRB) and gamma (TRG) loci in this ruminant species. RESULTS: Our analyses revealed that although the organization of the goat TRB locus is broadly similar to that of the other artiodactyl species, with three in-tandem D-J-C clusters located at the 3' end, a complex and extensive series of duplications have occurred in the V genes at the 5' end, leading to a marked expansion in the number of the TRBV genes. This phenomenon appears to be a feature of the ruminant lineage since similar gene expansions have also occurred in sheep and cattle. Likewise, the general organization of the goat TRG genes is typical of ruminant species studied so far, with two paralogous TRG loci, TRG1 and TRG2, located in two distinct and distant positions on the same chromosome as result of a split in the ancestral locus. Each TRG locus consists of reiterated V-J-J-C cassettes, with the goat TRG2 containing an additional cassette relative to the corresponding sheep and cattle loci. CONCLUSIONS: Taken together, these findings demonstrate that strong evolutionary pressures in the ruminant lineage have selected for the development of enlarged sets of TRB and TRG genes that contribute to a diverse T cell receptor repertoire. However, differences observed among the goat, sheep and cattle TRB and TRG genes indicate that distinct evolutionary histories, with independent expansions and/or contractions, have also affected each ruminant species.

Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats.

Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998 ± 0.001 and 0.028 ± 0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.

Gastrointestinal nematode infections in goats: differences between strongyle faecal egg counts and specific antibody responses to Teladorsagia circumcincta in Nera di Verzasca and Alpine goats.

Strongylida are gastrointestinal nematodes (GIN) of greatest importance in small ruminants throughout the world. Differences in resistance and resilience to GIN among goat breeds were reported. This study aims to investigate the mechanism underlying the breed-associated differences using a cosmopolitan (Alpine, AB) and an autochthonous (Nera di Verzasca, NV) goat breed. At first, fifteen goats from the same herd (NV = 7, AB = 8) at day 0 were infected with infective larvae (L3) of mixed GIN. From the 15th day post-infection (DPI), individual parasite egg excretion (faecal egg counts, FEC) was performed on all goats, once per week, until the 63rd DPI. Afterwards, in goats under field conditions (30 AB and 30 NV reared on the same farm), individual faecal and blood samples were collected; FEC-specific antibody and PCV levels were explored. In goats with experimental GIN infection, mean eggs per gram of faeces (EPG) values were consistently lower in NV goats. In goats with natural GIN infection, EPG and prevalence values showed high variability in both breeds; among individual variables, breed had a significant influence on EPG. Further, PCV and anti-T. circumcincta IgA levels were influenced by the breed. Lower PCV values were also associated with higher strongyle EPG in AB goats, and anti-T. circumcincta IgA levels were influenced by both strongyle EPG and breed, with IgA levels being higher in AB vs. NV goats and positively associated with EPG. Neither EPG nor breed had any influence on IgE levels. Both studies on experimental and natural infection confirmed that goats of NV are more resistant to infection with gastrointestinal nematodes.

Skin transcriptome reveals the periodic changes in genes underlying cashmere (ground hair) follicle transition in cashmere goats.

BACKGROUND: Cashmere goats make an outstanding contribution to the livestock textile industry and their cashmere is famous for its slenderness and softness and has been extensively studied. However, there are few reports on the molecular regulatory mechanisms of the secondary hair follicle growth cycle in cashmere goats. In order to explore the regular transition through the follicle cycle and the role of key genes in this cycle, we used a transcriptome sequencing technique to sequence the skin of Inner Mongolian cashmere goats during different months. We analyzed the variation and difference in genes throughout the whole hair follicle cycle. We then verified the regulatory mechanism of the cashmere goat secondary hair follicle growth cycle using fluorescence quantitative PCR. RESULTS: The growth cycle of cashmere hair could be divided into three distinct periods: a growth period (March-September), a regression period (September-December), and a resting period (December-March). The results of differential gene analyses showed that March was the most significant month. Cluster analysis of gene expression throughout the whole growth cycle further supported the key nodes of the three periods of cashmere growth, and the differential gene expression of keratin corresponding to the ground haircashmere growth cycle further supported the results from tissue slices. Quantitative fluorescence analysis showed that KAP3-1, KRTAP 8-1, and KRTAP 24-1 genes had close positive correlation with the cashmere growth cycle, and their regulation was consistent with the growth cycle of cashmere. CONCLUSION: The growth cycle of cashmere cashmere could be divided into three distinct periods: a growth period (March-September), a regression period (September-December) and a resting period (December-March). March was considered to be the beginning of the cycle. KAP and KRTAP showed close positive correlation with the growth cycle of secondary hair follicle cashmere growth, and their regulation was consistent with the cashmere growth cycle. But hair follicle development-related genes are expressed earlier than cashmere growth, indicating that cycle regulation could alter the temporal growth of cashmere. This study laid a theoretical foundation for the study of the cashmere development cycle and provided evidence for key genes during transition through the cashmere cycle. Our study provides a theoretical basis for cashmere goat breeding.

Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex.

Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.

Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq).

Circular RNA (circRNA) is endogenous non-coding RNA (ncRNA) with a covalently closed circular structure. It is mainly generated through RNA alternative splicing or back-splicing. CircRNA is known in the majority of eukaryotes and very stable. However, knowledge of the circRNA involved in regulating cashmere fineness is limited. Skin samples were collected from Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) during the anagen period. For differentially expressed circRNAs, RNA sequencing was performed, and the analysis led to an identification of 17 up-regulated circRNAs and 15 down-regulated circRNAs in LCG compared with MCG skin samples. In order to find the differentially expressed circRNAs in LCG, we carried out qPCRs on 10 candidate circRNAs in coarse type skin of LCG (CT-LCG) and fine type skin of LCG (FT-LCG). Four circRNAs: ciRNA128, circRNA6854, circRNA4154 and circRNA3620 were confirmed to be significantly differential expression in LCG. Also, a regulatory network of circRNAs-miRNAs was bioinformatically deduced and may help to understand molecular mechanisms of potential circRNA involvement in regulating cashmere fineness.

PRNP gene polymorphisms in main indigenous Turkish goat breeds.

The polymorphisms of the PRNP gene influence the susceptibility to scrapie in goats. In this study, caprine PRNP gene was analysed in a total of 249 individuals from three main indigenous goat breeds of Turkey: Anatolian Black, Angora and Kilis. We focused on the Anatolian Black breed, which represents 97% of the goat population in Turkey and compared the data of samples originated from different geographical regions. Eight polymorphisms were determined, given rise to 12 haplotypes. Allele, genotype and haplotype frequencies of the polymorphisms at codons 142, 143, 146, 154, 171, 211, 222 and 240 were calculated. Alleles associated to resistance to scrapie were found to be relatively rare in all breeds. The resistance allele 222K was absent in Turkish breeds. Other resistance-associated alleles: 146D, 146S, 154H and 171R were observed with low frequencies. The results of this study, which cover the mainly bred indigenous goats in Turkey, present the distribution of PRNP polymorphisms. Very low frequencies of resistance-associated alleles show the susceptibility to scrapie. The resistance-associated alleles S and D of codon 146 might be accepted as candidate alleles, due to their relative higher frequencies observed in the present study. A breeding program aiming to increase particularly the frequency of 146S might be applied. Predictions about impacts of a long-term breeding programme based on low initial allele frequencies and regarding its possible adverse effects are warranted. Our results might be a database for future breeding programmes, which should be carefully designed with adequate levels of genetic resistance and acceptable timeframe.

Assessing possible hybridization among managed Nubian ibex in North America.

Hybridization among closely related species is a concern in zoo and aquarium populations where unpedigreed animals are frequently exchanged with the private sector. In this study, we examine possible hybridization in a group of Nubian ibex (Capra nubiana) imported into the Association of Zoos and Aquariums' (AZA) Species Survival Program (SSP) from a private institution. These individuals appeared smaller in stature than adult SSP Nubian ibex and were excluded from breeding recommendations over the concern that they were hybrids. Twenty-six microsatellites were used to rule out recent hybridization with domestic goats, Siberian ibex (Capra sibirica), and Alpine ibex (Capra ibex). We argue that natural phenotypic variation across the large geographic range of Nubian ibex may account for the small stature of the imported ibex, as private institutions may have historically acquired individuals from locations that differed from the SSP founders. However, the imported Nubian ibex appeared genetically differentiated from the SSP Nubian ibex and may represent a source of genetic variation for the managed population.

Identification of the complete coding cDNAs and expression analysis of B4GALT1, LALBA, ST3GAL5, ST6GAL1 in the colostrum and milk of the Garganica and Maltese goat breeds to reveal possible implications for oligosaccharide biosynthesis.

BACKGROUND: Milk sialylated oligosaccharides (SOS) play crucial roles in many biological processes. The most abundant free SOS in goat's milk are 3'sialyllactose (3'-SL), 6'sialyllactose (6'-SL) and disialyllactose (DSL). The production of these molecules is determined genetically by the expression of glycosyltransferases and by the availability of nucleotide sugar substrates, but the precise mechanisms regulating the differential patterns of milk oligosaccharides are not known. We aimed to identify the complete cDNAs of candidate genes implicated in SOS biosynthesis (B4GALT1, LALBA, ST3GAL5, ST6GAL1) and to analyse their expression during lactation in the Garganica and Maltese goat breeds. Moreover, we analysed the colostrum and milk contents of 3'-SL, 6'-SL and disialyllactose (DSL) and the possible correlations between expressed genes and SOS. RESULTS: We identified the complete coding cDNAs of B4GALT1 (HQ700335.1), ST3GAL5 (KF055858.2), and ST6GAL1 (HQ709167.1), the single nucleotide polymorphism (SNPs) of these genes and 2 splicing variants of the ST6GAL1 cDNA. RT-qPCR analysis showed that LALBA and ST6GAL1 were the genes with the highest and lowest expression in both breeds, respectively. The interaction effects of the breeds and sampling times were associated with higher levels of B4GALT1 and ST3GAL5 gene expression in Garganica than in Maltese goats at kidding. B4GALT1, LALBA, and ST3GAL5 gene expression changed from kidding to 60 and 120 days in Maltese goats, while in Garganica goats, a difference was observed only for the LALBA gene. Breed and lactation effects were also found for SOS contents. Positive correlations of B4GALT1, LALBA, ST3GAL5, and ST6GAL1 with 3'-SL/6'SL and DSL were found. CONCLUSIONS: The genetic effect on the oligosaccharide content of milk was previously highlighted in bovines, and this study is the first to investigate this effect in two goat breeds (Garganica and Maltese) during lactation. The genetic variability of candidate genes involved in SOS biosynthesis highlights their potential role in affecting gene expression and ultimately biological function. The investigation of gene regulatory regions as well as the examination of other sialyltransferase genes will be needed to identify the genetic pattern leading to a higher SOS content in the autochtonous Garganica breed and to protect it using a focused breeding strategy.

Whole genome analysis of Black Bengal goat from Savar Goat Farm, Bangladesh.

OBJECTIVES: Single nucleotide polymorphisms (SNPs) play critical roles in genetic diversity and disease. Many traits and diseases are linked with exonic SNPs that are significant for gene function, regulation or translation. This study focuses on SNPs that potentially act as the genetic basis for desirable traits in the Black Bengal Goat. This variety of goat is native to South Asia, and is identified as one of the most commercially important meat producing animals in the world. The aim of this study was to sequence the genome of Black Bengal Goats and identify SNPs that might play a significant role in determining meat quality in the organism. The study focuses on exonic SNPs for their greater likelihood of affecting the final translated protein product. RESULTS: Approximately 76,000 exonic variants were identified in the study. After filtration using a Wilcoxon test based score, the number came down to 49, 965 which were found to be distributed in 11,568 genes. The functional pathways affected by these variations included fatty acid metabolism and degradation, which are important processes that influence meat quality.

Differential expression and characterization of ATP1A1 exon17 gene by high resolution melting analysis and RT-PCR in Indian goats.

The investigation was carried out to analyse the genetic polymorphism and gene expression of ATP1A1 gene in four different Indian goat breeds by using high resolution melting (HRM) and real time-PCR. ATPase is electro-genic ion pump which is maintains the balance of sodium and potassium ions in animal cells. The transport of Na+& K+ is variable at cellular level during extreme hot period. Therefore, susceptible and tolerant animals were selected based on the physiological responses during hot period. Blood samples were collected from individuals, DNA was isolated. The 300 bp fragment of ATP1A1 gene was amplified by PCR and HRM genotyping was performed. The melting curves were analysed, differential temperature-shift plot showed three different genotypes in all the analysed samples. Out of the 135 samples, the distribution percentages were 55.56% (AA/blue), 33.33% (AC/red) and 11.11% (CC/green). The sequence variation revealed a SNP at 143rd position (A>C). The nucleotide diversity was 0.695 ± 0.403, 0.732 ± 0.424, 0.662 ± 0.433 and 0.687 ± 0.398 in Barbari, Jamunapari, Jakharna and Sirohi, respectively. The respiration rate (RR) was significantly different (P < 0.05) between AA and AC (t = 1.875, df = 38) genotype and heart rate (HR) was significantly different (P < 0.05) between AA and CC genotype. The relative expression pattern of ATP1A1 in SNP variants and non-variants animal tissues showed 19.09 and 6.93 fold higher than control (non-variant), respectively. Jamunapari showed higher fold value of ATP1A1 gene in comparison to Barbari, Jakharna and Sirohi. However, the heat stress-susceptible phenotype had significantly higher gene expression than stress-tolerant in all the breeds. The variation may be used as a marker for selection on the basis of physiological parameters and expression of ATP1A1 gene in goats indicating the specificity of expression in each tissue.

Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics.

Indigenous goats make significant contributions to Cameroon's national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO (0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

Genetic diversity and population structure in multiple Chinese goat populations using a SNP panel.

Information about genetic diversity and population structure among goat breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds. Here, we measured genetic diversity and population structure in multiple Chinese goat populations, namely, Nanjiang, Qinggeda, Arbas Cashmere, Jining Grey, Luoping Yellow and Guangfeng goats. A total of 193 individuals were genotyped for about 47 401 autosomal single nucleotide polymorphisms (SNPs). We found a high proportion of informative SNPs, ranging from 69.5% in the Luoping Yellow to 93.9% in the Jining Grey goat breeds with an average mean of 84.7%. Diversity, as measured by expected heterozygosity, ranged from 0.371 in Luoping Yellow to 0.405 in Jining Grey goat populations. The average estimated pair-wise genetic differentiation (FST ) among the populations was 8.6%, ranging from 0.2% to 16% and indicating low to moderate genetic differentiation. Principal component analysis, genetic structure and phylogenetic tree analysis revealed a clustering of six Chinese goat populations according to geographic distribution. The results from this study can contribute valuable genetic information and can properly assist with within-breed diversity, which provides a good opportunity for sustainable utilization of and maintenance of genetic resource improvements in the Chinese goat populations.

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.

Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat (Capra species) breeds for the production of dairy, cashmere, and meat.

Background: The domestication of wild goats and subsequent intensive trait-driven crossing, inbreeding, and selection have led to dramatic phenotypic purification and intermediate breeds for the high-quality production of dairy, cashmere wool, and meat. Genomic resequencing provides a powerful means for the direct identification of trait-associated sequence variations that underlie molecular mechanisms of domestication. Results: Here, we report our effort to define such variations based on data from domestic goat breeds (Capra aegagrus hircus; five each) selected for dairy, cashmere, and meat production in reference to their wild ancestors, the Sindh ibex (Capra aegagrus blythi; two) and the Markhor (Capra falconeri; two). Using ∼24 million high-quality single nucleotide polymorphisms (SNPs), ∼1.9 million insertions/deletions, and 2,317 copy number variations, we define SNP-desert-associated genes (SAGs), domestic-associated genes (DAGs), and trait-associated genes (TAGs) and attempt to associate them with quantitative trait loci (QTL), domestication, and agronomic traits. A greater majority of SAGs shared by all domestic breeds are classified into Gene Ontology categories of metabolism and cell cycle. DAGs, together with some SAGs, are most relevant to behavior, immunity, and trait specificity. Whereas, TAGs such as growth differentiation factor 5 and fibroblast growth factor 5 for bone and hair growth, respectively, appear to be directly involved in growth regulation. Conclusions: When investigating the divergence of Capra populations, the sequence variations and candidate function-associated genes we have identified provide valuable molecular markers for trait-driven genetic mapping and breeding.