Domestic Goat Breeds Research Articles

GOAT FARMING IN THE VRBAS BANOVINA

The aim of the paper is to analyze goat farming in the Vrbas Banovina based on published and unpublished sources and available literature. In certain areas of the Kingdom of Yugoslavia, goat farming was a major branch of stockbreeding. The portion of the population that did not have enough land to sustain a cow was able to successfully keep two to three goats. For the poorer population in the country, goats were the most significant domesticated animals, and they provided a substantial income. The paper compares the number of goats in certain European countries, the Kingdom of Yugoslavia, its banovinas, and the districts of the Vrbas Banovina. It also focuses on the lives of the people, the traits of the domestic Balkan goat, goat breeds, goat housing and feeding, stockbreeding trends, goat diseases and restrictions on keeping goats.

A Mitochondrial DNA-based Molecular Phylogenetics Study of the Mahalli Goat as a New Animal Genetic Resource in Southern Anatolia in Turkey

Background: The Karacadağ Mountains are of extinct volcanic origin and cover a large area in the triangle between Diyarbakır (Center, Nar and Ergani districts), Şanlılurfa (Siverek and Viranşehir districts) and Mardin (Derik district). Agricultural activities are limited due to the stony structure of the region; therefore, small animal husbandry is intensively practiced in the villages of the region. Mahalli goats, which are morphologically new domestic goats, are distinguished from other domestic goats by their spiral horn structure. They are not only resistant to cold weather conditions, but also resistant to diseases. Therefore, present study aimed to determine the genetic diversity and phylogenetic relationships of Mahalli goats in Diyarbakır region. Methods: The study was carried out at Şanlıurfa, Harran University of Agricultural Faculty, Laboratory of Animal Biotechnology and Molecular Genetics, in 2019-2020. Out of 24 Mahalli goats, forward and reverse primers were used to amplify the 598 bp region over the mtDNA D-loop region encompassing the 481 bp most variable region (HVR1). Analysis of goat D-loop sequences revealed 481 regions of 0.378 G+C, 97 polymorphic regions and 19 haplotypes. The phylogenetic analysis of Mahalli goats was carried out using molecular genetic techniques. Result: As a result of data analysis, both haplotype diversity (HD) and nucleotide diversity (ND) were calculated to be 1.000±0.0039 and 0.0375±0.00209, respectively. The genetic distance between the haplotypes of Mahalli goat ranged from 0.003 to 0.087 and the genetic distance between the haplotypes of Mahalli goat and other domestic goat breeds in Turkey ranged from 0.016 to 0.027. All 19 haplotypes used in this study were represented in the lineage A phylogenetic tree.

Growth hormone gene polymorphism in domestic and wild goat breeds in Kurdistan region of Iraq using PCR-RFLP and SNP markers

Growth hormone gene polymorphism in domestic and wild goat breeds in Kurdistan region of Iraq using PCR-RFLP and SNP markers

Melhorando as características reprodutivas e de crescimento em cabras nativas criadas em sistema de pequenas propriedades

ABSTRACT: Goat breeding is an economic activity carried out in the rural areas of the Eastern Mediterranean region of Türkiye. The small ruminants breeding project carried out in extensive farmer conditions was a project which aimed to improve the quality and quantity of meat and milk yields of domestic goat breeds of Anatolia since 2015. The genetic improvement study of indigenous Hair goats was started in 2015 and ended in 2020, using 5985 does and 252 bucks, with the participation of 60 local volunteer farmers in the rural farming system of Eastern Anatolia of Türkiye. At the end of the study, it was found that the birth rate, twinning rate, prolificacy, litter size, and survival rate varied between, 81.88 to 98.18%, 5.26 to 13.54%, 103.00 to 111.00%, 1.11 to 1.27 and 92.67% to 99.06%, by years respectively. As a result of the breeding study, it was determined that the birth weight, weaning weight, and daily body weight gain of the offspring were increased from 2.60 to 3.07 kg, from 8.21 to 10.77 kg, and from 107.74 to 149.15 g, respectively. It was determined that the growth characteristics of kids differed significantly over the years (P < 0.001). As a result of this study, it was determined that production based on local gene resources with improved genetic capacity in rural areas is important for sustainability. Simple recording schemes for the objective assessment of performance traits and planned mating schemes will help enhance animals’ production performances in traditional farming systems.

Caprine Myostatin Gene Polymorphism in Domestic and Wild Goat Breeds in Duhok Province/Kurdistan Region of Iraq Using PCR-RFLP and SNP Markers

In Iraq generally and Kurdistan region specifically, goats are an important resource for meat and milk production. It is well known that Myostatin genes (MSTN) have the essential role in growth and development due to its crucial involvement in muscle growth. The goal of this research was to reveal the polymorphism of MSTN gene in different Capra hircus breeds (native, Shami, Meriz and Kamori goat) and in wild mountain goat (Capra aegagrus) via PCR-RFLP technique and direct seqencing The MSTN (exon 1) polymorphisms were investigated in all breeds, MSTN-Dra I/RFLP revealed three genotypes AA and BB were homozygous and AB was heterozygous. The calculated genotype frequencies were 0.270, 0.368 and 0.362 for AA, BB and AB genotype respectively. The allelic frequency was 0.451 for the A allele and 0.549 for the B allele. The average of the observed heterozygosity was 0.362 and the observed homozygosity was 0.638. The sequence data of MSTN gene of Native and Shami goats revealed 31 SNPs in nonfunctional region. In addition, in exon region there was 1 SNPs in both breed samples which did not change amino acid sequence and its silence mutation. In conclusion, the result of PCR-RFLP and SNP experiments obtained in this investigation were evaluated as very useful in genotype analysis of local goat breeds/populations. Thus, DNA polymorphisms in the Myostatin gene could be used as reliable genetic marker in breeding programs in this region.

Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.

Molecular investigations on the Rajanpuri strain of Beetal goat breed of Pakistan by complete mtDNA displacement region and microsatellite markers

The mitochondrial DNA sequences of DNA-D loops (mtDNA) from 105 individuals (11 Beetal goat Rajanpuri strains and 94 sequences extracted from GenBank) from 19 geographically and phenotypically defined domestic goat breeds in Pakistan were analysed in this experiment. In this study, we examined variability and molecular phylogeny of breeds. A total of 81 haplotypes were observed in 105 individuals, with a haplotype diversity of 0.984±0.006 and nucleotide diversity of 0.03953±0.00843. Phylogenetic analysis based on the mtDNA hyper variable segment (HVI) of the control region (481 bp), showed four mtDNA haplogroups (A, B1, C, and D) identified in Pakistani domestic goats, in which haplogroup A (84.11%) was dominant and widely distributed among all investigated breeds. The study revealed that all Rajanpuri strain haplotypes belonged to haplogroup A. The Rajanpuri is a rare local strain of Beetal goat breed located in western Punjab province of Pakistan. The results of genetic diversity based on 11 microsatellite loci revealed allelic diversity (3.6363) and high genetic diversity (0.8342) in the examined Rajanpuri goat breeds. The analysis for signature bottleneck events, using three models, revealed significant deviation of Rajanpuri goats from mutation drift equilibrium. The qualitative test of mode shift analysis also supported the results obtained under three models, indicating the presence of a recent genetic bottleneck in the Rajanpuri strain. This study provides the first information on the mtDNA architecture, genetic diversity and bottleneck analysis, which will be useful in the conservation and management of the highly valued Rajanpuri goat.

Capture Sequencing to Explore and Map Rare Casein Variants in Goats.

Genetic variations in the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3 have obtained substantial attention since they affect the milk protein yield, milk composition, cheese processing properties, and digestibility as well as tolerance in human nutrition. Furthermore, milk protein variants are used for breed characterization, biodiversity, and phylogenetic studies. The current study aimed at the identification of casein protein variants in five domestic goat breeds from Sudan (Nubian, Desert, Nilotic, Taggar, and Saanen) and three wild goat species [Capra aegagrus aegagrus (Bezoar ibex), Capra nubiana (Nubian ibex), and Capra ibex (Alpine ibex)]. High-density capture sequencing of 33 goats identified in total 22 non-synonymous and 13 synonymous single nucleotide polymorphisms (SNPs), of which nine non-synonymous and seven synonymous SNPs are new. In the CSN1S1 gene, the new non-synonymous SNP ss7213522403 segregated in Alpine ibex. In the CSN2 gene, the new non-synonymous SNPs ss7213522526, ss7213522558, and ss7213522487 were found exclusively in Nubian and Alpine ibex. In the CSN1S2 gene, the new non-synonymous SNPs ss7213522477, ss7213522549, and ss7213522575 were found in Nubian ibex only. In the CSN3 gene, the non-synonymous SNPs ss7213522604 and ss7213522610 were found in Alpine ibex. The identified DNA sequence variants led to the detection of nine new casein protein variants. New variants were detected for alpha S1 casein in Saanen goats (CSN1S1∗C1), Bezoar ibex (CSN1S1∗J), and Alpine ibex (CSN1S1∗K), for beta and kappa caseins in Alpine ibex (CSN2∗F and CSN3∗X), and for alpha S2 casein in all domesticated and wild goats (CSN1S2∗H), in Nubian and Desert goats (CSN1S2∗I), or in Nubian ibex only (CSN1S2∗J and CSN1S2∗K). The results show that most novel SNPs and protein variants occur in the critically endangered Nubian ibex. This highlights the importance of the preservation of this endangered breed. Furthermore, we suggest validating and further characterizing the new casein protein variants.

42 Genetic differentiation of Russian goats and wild relatives based on microsatellite loci

Abstract Goat breeding is a traditional livestock industry for many regions of Russia. Due to unpretentiousness and high adaptive qualities, the Karachai, Dagestan wool and Dagestan down breeds are widespread in the North Caucasus. Moreover, their uniqueness is determined by sharing a common habitat with their wild relatives, West Caucasian and Dagestani turs, thus forming hybrid zones. The aim of the research was to study allele pool and interbreed differentiation of domestic goat breeds and wild relatives by microsatellites. Research was performed based on 16 loci on the ABI 3130xl analyzer. Population genetic characteristics were calculated in GenAlEx 6.5, and the phylogenetic tree was constructed in Populations 1.2.30 and SplitsTree 4.14.5. The sample collection included goat breeds (n = 226): Karachai (KRCH), Dagestan down (DAGD), Dagestan wool (DAGW) (North Caucasus), Soviet wool (SOVW) (Siberia), Orenburg (OREN) (South Ural), and wild goats (n = 72). Wild goats comprised mountain goats: Siberian goats (Capra sibirica) from the Altai, Tajikistan, Kyrgyzstan and the Himalayas; bezoar goats (Capra aegagrus) from Turkey and Pakistan; and tur (Capra caucasica) from the West Caucasus (Kuban), Central Caucasus, and East Caucasus (Dagestan). The Karachai breed was characterized by the highest level of genetic diversity: the average number of alleles per locus (NA) and allelic richness (AR) were 9,154 and 7,713, respectively, while these indices varied from 6,538 to 7,538 and from 6,425 to 7,538 (Table 1) in other breeds, respectively. The values of genetic distances showed differentiation of Karachai, Dagestan down and Dagestan wool breeds from Orenburg and Soviet wool breeds (Table 2). The formation of three clusters was established. The first one included subspecies of the Caucasian tur, the second one comprised Siberian goats, and the third contained domestic goats. Bezoar goats were in the root of the third cluster that confirmed their participation as an ancestral form of domestic goats.

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

BackgroundCopy 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.ResultsWe 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 FST 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 (FST = 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.ConclusionWe 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.

Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus).

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14–20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion–deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide FST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.

Genetic diversity, population structure of seven Indian domestic goat breeds based SNPs identified in CAPN1 gene

The micromolar calcium-activated neutral protease (CAPN1) gene encodes μ-calpain that degrades myofibril proteins under the post-mortem conditions which appears to be the primary enzyme in the postmortem tenderization process, hence affecting the meat quality. Objective of this study was to analyze genetic polymorphism of the CAPN1 gene in seven diverse Indian goat breeds. Direct DNA sequencing was carried out to identify the genetic polymorphisms in 84 unrelated goats representing seven different goat breeds (Barbari, Beetal, Ganjam, Sirohi, Black Bengal, Osmanabadi and Malabari). Six single nucleotide polymorphisms (SNPs) were identified in CAPN1 gene intron 17. The observed heterozygosity (Ho) was highest (0.50) in Sirohi and Osmanabadi (0.42) breeds and lowest in Black Bengal (0.06) breed. The expected heterozygosity (He) was highest (0.45) in Sirohi followed by Osmanabadi (0.37), Barbari (0.34) and Beetal (0.37). The allele frequencies ranged from 0.083 to 0.917 and the major allele frequencies ranged from 0.595 (locus 6499 T/C) to 0.917 (locus 6529 T/C). In Black Bengal, polymorphism at all theloci was fixed with the exception of 6417 T/G and 6533C/G. The identity values oscillated from 0.7866 to 0.9593. The Nei's genetic distances were below 0.0294. Genetic diversity among different goat meat breeds indicates possible role in meat quality trait. Allelic diversity at this locus could be used in further for the association between gene polymorphism and enzyme activity as well as caprine meat quality traits.

GENETIC DIVERSITY OF LEPTIN GENE INTRON 2 IN WILD AND NATIVE AND EXOTIC GOAT BREEDS IN IRAN

The aim of this study was to investigate the intron 2 of leptin gene polymorphism in wild, native and exotic goat breeds in Iran using PCR-RFLP. Blood samples were collected from 14 wild and domestic goat breeds including (Cashmere Abadeh, Torki-Ghashghaei, Naeini, Robati, Nadoushani, Adani, Shahrbabaki, Birjandi, China goat, Sannen, Pakistani, Raeini cashmere, Najdi and Wild goat) and then the genomic DNA was extracted. A 422bp fragment from intron 2 of the leptin gene was amplified. PCR products were digested by Sau3AI restriction enzyme and were separated and visualized on the agarose gel. Three genotypes including MM, Mm and mm with genotype frequency of 94%, 1% and 5%, respectively, were observed in the studied populations. The number of observed alleles, number of the effective alleles, Nei’s Index and Shanon’s Index were 2, 1.10, 0.09 and 0.19, respectively. The studied populations were not found to be in a Hardy-Weinberg equilibrium. Our investigation demonstrated that MM genotype and M allele had a very high frequency (0.94 and 0.95, respectively) in Iranian goats. Hence, it can be concluded that this finding can provide basis for selection when considering evolution and differentiation among breeds, however further studies should be carried out on a larger population of different domestic and wild breeds to verify the final conclusions.

Comparative genome analyses reveal the unique genetic composition and selection signals underlying the phenotypic characteristics of three Chinese domestic goat breeds

BackgroundAs one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, the genetic loci that underlie phenotypic variations in domestic goats are largely unknown, particularly for economically important traits. In this study, we sequenced the whole genome of 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) and downloaded the genome sequence data of 30 goats from five other breeds (four non-Chinese and one Chinese breed) and 21 Bezoar ibexes to investigate the genetic composition and selection signatures of the Chinese goat breeds after domestication.ResultsBased on population structure analysis and FST values (average FST = 0.22), the genetic composition of Chengdu Brown goats differs considerably from that of Bezoar ibexes as a result of geographic isolation. Strikingly, the genes under selection that we identified in Tibetan Cashmere goats were significantly enriched in the categories hair growth and bone and nervous system development, possibly because they are involved in adaptation to high-altitude. In particular, we found a large difference in allele frequency of one novel SNP (c.-253G>A) in the 5′-UTR of FGF5 between Cashmere goats and goat breeds with short hair. The mutation at this site introduces a start codon that results in the occurrence of a premature FGF5 protein and is likely a natural causal variant that is involved in the long hair phenotype of cashmere goats. The haplotype tagged with the AGG-allele in exon 12 of DSG3, which encodes a cell adhesion molecule that is expressed mainly in the skin, was almost fixed in Tibetan Cashmere goats, whereas this locus still segregates in the lowland goat breeds. The pigmentation gene KITLG showed a strong signature of selection in Tibetan Cashmere goats. The genes ASIP and LCORL were identified as being under positive selection in Jintang Black goats.ConclusionsAfter domestication, geographic isolation of some goat breeds has resulted in distinct genetic structures. Furthermore, our work highlights several positively selected genes that likely contributed to breed-related traits in domestic goats.

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.

BackgroundThe 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.ResultsHere, 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.ConclusionsWhen 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.

Serological evidence of foot-and-mouth disease virus infection in goat breeds in the Samsun province of Turkey

Foot-and-mouth disease (FMD) is one of the major endemic trans-boundary livestock diseases of socio-economic importance in Turkey and worldwide. Goats constitute the third largest susceptible population of domestic livestock in Turkey. FMD surveillance and control strategies in the country largely ignore small ruminants, known to be critical in the epidemiology of the disease. In this study, blood samples were randomly collected from different domestic goat breeds (Anatolian black goat, Maltese and Saanen). The material consisted of 368 domestic goats, including 121 Anatolian black, 125 Maltese and 122 Saanen goats from Samsun province. The serum samples were examined for the presence of antibodies to foot and mouth disease virus using non structural proteins (NSPs) competitive enzyme-linked immunosorbent assay (ELISA). Out of 368 serum samples examined, 12 (3.26%) were positive for FMD. Seropositivity rates in Anatolian black, Saanen and Maltese breeds were 0.83%, 0.82% and 8.00% for FMD, respectively. Although, seropositivity rate in Maltese goat breed was higher than others, this result was not attributed to breed susceptibility. The results of the investigation indicate that FMD is less widespread in goats than sheep and cattle in Samsun province. The results, supported for the first time in Turkey the hypothesis that goats act as a potential reservoir of FMD virus and thus have a role in the epidemiology of FMD.

Genetic Structure of Chinese Indigenous Goats and the Special Geographical Structure in the Southwest China as a Geographic Barrier Driving the Fragmentation of a Large Population

BackgroundChina has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers.Methodology/Principal FindingsForty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (HS of 0.644) and high population diversity at the species level (HT value of 0.737) were estimated. Significant moderate population differentiation was detected (FST value of 0.129). Significant excess homozygosity (FIS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China.Conclusions/SignificanceOur results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats.

Genetic diversity and molecular phylogeography of Chinese domestic goats by large-scale mitochondrial DNA analysis

Mitochondrial DNA (mtDNA) D-loop sequences of 666 individuals (including 109 new individuals, 557 individuals retrieved from GenBank) from 33 Chinese domestic goat breeds throughout China were used to investigate their mtDNA variability and molecular phylogeography. The results showed that all goat breeds in this study proved to be extremely diverse, and the average haplotype diversity and nucleotide diversity were 0.990 ± 0.001 and 0.032 ± 0.001, respectively. The 666 sequences gave 326 different haplotypes. Phylogenetic analyses revealed that there were 4 mtDNA haplogroups identified in Chinese domestic goats, in which haplogroup A was predominant and widely distributed. Our finding was consistent with archaeological data and other genetic diversity studies. Amova analysis showed there was significant geographical structuring. Almost 84.31% of genetic variation was included in the within-breed variance component and only 4.69% was observed among the geographic distributions. This genetic diversity results further supported the previous view of multiple maternal origins of Chinese domestic goats, and the results on the phylogenetic relationship contributed to a better understanding of the history of goat domestication and modern production of domestic goats.

Mitochondrial DNA Diversity in Three Sudanese Goat Breeds

This study was conducted on 45 heads (15 of each breed) of three Sudanese domestic goat breeds (Desert goat, Nubian goat and Taggar goat) to pursue complete mitochondrial DNA analysis using PCR-RFLP method to detect the mitochondrial DNA diversity of two mit-DNA haplogroups, lineage A and lineage D. The results revealed that most individuals of the three breeds belonged to lineage A with frequencies 0.2 of Desert goats, 0.6 of Nubian goats and 0.6 of Tagar goats. Some of the individuals belonged to modified lineage A with frequencies 0.2 of Desert goats, 0.2 of Nubian goats and 0.2 of Tagar goats; no individual of each belonged to lineage D. In conclusion, the appearance of individuals that belonged to modified lineage A in the different goat breeds might be due to mutation resulted from insertion or deletion of events and might a criterion of the Sudanese indigenous goat breeds. However this suggestion needs more confirmative analysis.

Genetic Structuring of Nine Indian Domestic Goat Breeds Based on SNPs Identified in IGF-1 Gene

The caprine Insulin like Growth Factor1 (IGF1) gene was analyzed for identification of single nucleotide polymorphisms (SNPs) and genetic structuring of Indian goat breeds. A panel of 80 samples belonging to nine Indian goat breeds (Capra hircus) including three large sized breeds (Jamunapari, Beetal and Jakhrana); three medium sized breeds (Sirohi, Barbari, and Osmanabadi) and three small sized breeds (Black Bengal, Changthangi, and Gaddi) were screened for SNP identification and diversity analysis. The comparative gene sequence analysis of all the nine goat breeds studied revealed a total of 18 SNPs in IGF1 gene. All the nucleotide changes were found to be synonymous. The mean observed heterozygosity was found to be maximum (0.074) in Sirohi, Beetal, Osmanabadi, and Gaddi breeds of goat, whereas it is found to be minimum (0.019) in Black Bengal breed of goat. The rest of the breeds were intermediate in terms of heterozygosity. The same has been confirmed by allele frequency distribution across the studied loci. Barbari and Gaddi were found to be more differentiated (0.0123), Changthangi and Jamunapari were least differentiated (0.00110) based on Nei's genetic distance.