Indian Goat Breeds Research Articles

Genetic diversity and evolutionary significance of Cahi-DRB1 gene in Indian goat from semi-arid regions

Unlocking the genetic diversity of the Cahi-DRB1 gene in Indian goat breeds sheds light on their immune system's resilience. While extensive studies have elucidated MHC diversity in cattle and sheep, research on goats remains limited. Thus, this study aimed to investigate the genetic diversity of cahi-DRB1 across five goat breeds in India, encompassing a total of 233 individual goats. Using a PCR sequence-based typing approach, DRB1 fragments (285 bp) were amplified and sequenced. The PCR products were purified and sequenced. Amino acid variability within breeds was evaluated using the Wu-Kabat index at peptide-binding pockets. Selection analysis included assessing positive selection through relative rates of nonsynonymous and synonymous mutations, Z-test, and Tajima's test of neutrality. The findings revealed notable heterozygosity across breeds (mean: 100 %), with nucleotide content averaging 22.51 % for A, 18.62 % for T, 24.33 % for C, and 34.35 % for G. The GC content was rich (59.26 %) across breeds for the DRB1 region. The mean distance for DRB1 was highest in Barbari (0.20) and lowest in Osmanabadi goat (0.12), with a higher rate of transversions observed. The Wu-Kabat index assessments underscored substantial genetic variation within the peptide binding sites (PBS) of DRB1, with specific residues (12, 14, 33, 58, and 87) showing polymorphism relevant to antigen presentation. Positive selection pressure was evident across all breeds for the DRB1 locus (dN>dS), highlighting its evolutionary significance. The rich diversity of the DRB1 gene underscores the fitness of the population and the significance of this locus for future selection programs. These results highlight the highly polymorphic nature of the DRB1 locus in Indian goat breeds, emphasizing its crucial role in modulating immune responses. Consequently, our study offers valuable insights for developing targeted breeding strategies to enhance disease resistance in goats, thereby providing practical implications for sustainable livestock management.

Discovery and computational exploration of SNPs in GNRHR gene and their influence on protein structure and function in Indian goat breeds

This study focuses on identifying functional single nucleotide polymorphisms (SNPs) within the gonadotropin-releasing hormone receptor (GNRHR) gene and conducting subsequent in-silico analysis of their effects on protein structure and function in two distinct South Indian goat breeds, namely Attapady Black (n = 120) and Malabari goats (n = 180), known for their divergent prolificacy traits. Utilizing a DNA pool sequencing assay, ten SNPs were uncovered in the study population: c.-1129T>G, c.-1069A>G, c.-978A>C, c.-605A>G, c.-33A>G, c.-29T>G, c.48G>A, c.75G>A, c.209T>G, and c.*212A>G. Notably, two polymorphisms, c.-1129T>G and c.-33A>G, were novel. Additionally, two polymorphisms, c.-33A>G and c.-978A>C, were exclusive to Malabari goats. Analysis of upstream variants revealed modifications to transcription factor and micro-RNA (miRNA) binding sites, suggesting potential alterations in GNRHR expression. Of particular significance was the non-synonymous exonic variant at c.209T>G locus, resulting in methionine to arginine substitution at the 70th position within the first intracellular loop of the receptor protein. This amino acid change may have implications for the functional dynamics of the receptor as GnRHR intracellular loops are involved in G protein coupling thereby facilitation of downstream signalling pathways. The identified SNPs and their in-silico impact analysis contribute to our understanding of the molecular mechanisms underlying reproductive traits in these goat populations, with implications for future breeding strategies and genomic selection programs.

Genome-wide runs of homozygosity signatures in diverse Indian goat breeds.

The online version contains supplementary material available at 10.1007/s13205-024-03921-y.

Genome-wide runs of homozygosity in Indian goat breeds reared under small holder production system

Small holder goat production system is often constrained by high inbreeding due to small herd size and uncontrolled breeding. Runs of homozygosity (ROH), the long stretches of homozygous genomic DNA is the most reliable measure of autozygosity. The objective of present study was to investigate the number and coverage of ROH in the genome and to estimate the genomic inbreeding coefficient (FROH) in two divergent Indian goat breeds viz; Attappady Black and Malabari goats farmed under small holder production system. The genome-wide single nucleotide polymorphism (SNP) marker data obtained by Illumina SNP50 goat BeadChip genotyping of 48 goats (24 each of Attappady Black and Malabari goats) sampled from farmers flock in their respective breeding tract was utilised for ROH detection. The ROH of > 1 Mb was defined as tracts of homozygous genotypes with at least 15 SNPs and less than five missing SNPs. The ROH detection was carried out with PLINK 1.9 version. The proportion of goats lacking ROH (per cent) was 66.67 in Attappady Black and 39.13 in Malabari goats. The mean number and length of ROH of 1 Mb or more was higher in Malabari goats (2.1304 ± 0.6369 and 6.0016 ± 0.5271 Mb) compared to Attappady Black goats (0.4583 ± 0.1343 and 4.0197 ± 0.3755 Mb). Mean ± S.E of sum of ROH coverage of genome per individual (SROH) was 1.8423 ± 0.05976 and 8.8236 ± 1.2785 Mb in Attappady Black and Malabari goats, respectively and differed among the two breeds significantly (p ≤ 0.05). Analysis of the distribution of ROH according to their length showed that majority of the detected ROH were < 8 Mb in length in both breeds with no ROH of > 8 Mb in Attappady Black goats. Mean ± S.E of genomic inbreeding coefficient (FROH≥1 Mb) in per cent was 0.519 ± 0.19 and 0.07480 ± 0.0243 in Malabari goats and Attappady Black goats, respectively. The pattern of ROH estimated in the present analysis indicates the inbreeding history of the goats farmed under small holder production system. Results of present study indicate that both breeds are less consanguineous and showed no evidence of recent inbreeding.

Polymorphism of CSN2 Gene Exon 7 in Indonesian Dairy Goat Breeds

Milk production and composition are the main factors in the dairy industry. However, these traits are influenced by several factors, such as genetic factors. The CSN2 gene exon 7 is one of the genes that can affect the protein composition of goat milk. Several studies on the CSN2 gene exon seven have been conducted on Italian and Indian goat breeds, and their genetic variations have been found. Studies about CSN2 gene exon seven polymorphisms in Indonesia have been completed but found no variations. Therefore, this study aims to find genetic variations of CSN2 gene exon 7 using the Sanger Sequencing Method. Ninety-five blood samples of 66 Sapera, 15 Saanen, and 14 Etawa Grade goats were collected from the Livestock Research Center, Ciawi. Genetic diversity was calculated using PopGene32 programs. The results found two polymorphic SNPs in all three dairy goat breeds, namely g.8946C&gt;T and g.8956G&gt;A. Three genotypes found in SNP g.8946C&gt;T are CC, CT, and TT, while a new SNP g.8956G&gt;A found two genotypes (GG and GA). In conclusion, SNPs g.8946C&gt;T and g.8956G&gt;A are polymorphic. Additional research should be conducted to determine whether there is any association between these 2 SNPs and milk production and quality.

Design and validation of high-density SNP array of goats and population stratification of Indian goat breeds

Goats are the supporting pillars of rural economy contributing significantly to meat and milk production in India. It is a species targeted for fulfilling the interdependent goals of poverty reduction and creation of employment for supporting the rural income. The increased demand for goat products necessitates their genetic characterization and improvement to augment the production of native breeds. Bi-allelic, genome wide, densely placed single nucleotide polymorphism (SNP) markers are most suitable for this purpose. This paper describes the design and validation of an Affymetrix Axiom-based high-density (HD) SNP chip for goats. The array was designed using a panel of 225 samples from 15 diverse goat breeds of India. In total, more than 38 million high quality SNPs were subjected to stringent filtering and 626,975 SNPs were finally tiled on the array. The average coverage of SNPs in our chip is one SNP per four kilobase (kb), providing a denser coverage of the goat genome than previously available arrays. The HD chip (Axiom_Cahi) was validated by genotyping 443 samples from 26 indigenous goat breeds/populations. The results revealed 95.83% markers to be highly informative and polymorphic in Indian goats. Multivariate analysis indicated population structuring, as 15 breeds could be segregated using the designed array. Phylogenetic analysis suggested stratification of breeds by geographic proximity. This HD SNP chip for goats is a valuable resource for genomic selection, genome wide association as well as population genetic studies in goats.

Linkage disequilibrium and effective population size in Indian goat breeds

Genomic linkage disequilibrium (LD) is an important population diversity measure and an indicator determining the efficacy of genomic applications. The present population genomic study was carried out to comprehensively characterise the extent and pattern of LD in the two divergent Indian goat breeds namely, Attappady Black and Malabari goats reared under small holder production system. The LD was estimated using genome-wide single nucleotide polymorphism (SNP) marker data obtained by Illumina SNP50 goat BeadChip genotyping. The LD between adjacent SNPs across all autosomes measured as correlation coefficient (r2) in the studied population was low and mean ± standard deviation of LD were 0.0657 ± 0.0921 and 0.0661 ± 0.0911 for Attappady Black and Malabari goats, respectively. The LD varied significantly (p < 0.0001) among chromosomes, interaction between chromosome and breed and among marker intervals. The LD (r2) of 0.2 and 0.3 were extended up to 20 kb and 10 kb marker intervals, respectively. Based on the genomic data, Ne was estimated as 512.8198 in Malabari and 371.2220 in Attappady Black goats at 17 generations back. The weak LD observed in Indian goat breeds indicates increased diversity of these Indian goat breeds and also implies that denser SNP panel might be more beneficial for genomic applications.

Expression profile and association of ghrelin gene polymorphism with growth and litter traits in Indian goat breeds

Ghrelin (GHRL) is a 28 amino acid bioactive peptide influencing growth hormone secretion, regulation of energy homeostasis and appetite stimulation. The present investigation was undertaken to study the expression profile of the caprine ghrelin gene and to identify single nucleotide variations in caprine ghrelin gene to evaluate its association with production traits. Tissue samples of abomasum, lung, liver, spleen, fallopian tube and ovary were collected from six Malabari and Attappady Black adult goats to study the ghrelin gene expression pattern. Quantitative Real-Time PCR was used to find out the relative expression of ghrelin in various tissues. It was observed that there was a higher expression of ghrelin in the abomasal (3.67) tissues and the least expression in the liver (0.19) tissues. Significantly higher level of expression was noticed in Attappady Black than Malabari goats. Highly significant (p < 0.01) 4.07 fold upregulation was noticed in the ovary compared to the lung (3.85) and abomasum (3.80). A total of 176 Malabari and Attappady Black adult goats were screened for polymorphism using PCR-SSCP. Representative samples from different band patterns were sequenced. Two SNPs at the 9th position (C→A transversion) and at the 38th position (G→T transversion) in exon 4 and two SNPs at the 45th position (C→T transition) and 89th position (C→T transition) in intron 4 were identified. A significant association was observed between body measurement traits and the identified single nucleotide polymorphisms. The AB genotype demonstrated superior values over the AA genotype in body length and height for exon 4, while for intron 4 AA genotype was superior to the AB genotype. The AB genotype demonstrated higher values over the AA genotype for chest girth, CCI and TI. However, no association was found between body weight and litter size. The ghrelin gene may be used in marker-assisted selection for improving conformation traits in goats.

Association of Body Weight with Testicular and Semen Quality Parameters in Indian Goat Breeds

Association of Body Weight with Testicular and Semen Quality Parameters in Indian Goat Breeds

Evaluation of Bone Morphogenetic Protein-4 gene polymorphism for growth traits in Indian goat breeds

The genetic improvement of production traits can be made through marker assisted selection using a candidategene approach. Bone morphogenetic proteins (BMPs) are multifunctional growth factors that belong to thetransforming growth factor b (TGF-b) superfamily. This study aimed to detect the genetic polymorphism of BMP-4in different goat breeds by polymerase chain reaction-single strand confirmational polymorphism (PCR-SSCP) andassociation of polymorphic variants with growth traits. The amplified fragments of BMP4 gene of 380 bp size wereanalysed using SSCP in non-denaturing PAGE and the results showed the presence of two genotypes: AA (47-67%) and BB (33-53%) in Barbari, Sirohi and Black Bengal breed. The association of BMP-4 polymorphism withdifferent growth trait parameters showed non-significant effect of genotypes. However, some genotypes showednon-significant superiority over others. Further research on a large population is required to validate the role of theBMP-4 gene in goat growth traits.

Probiotic Lactic Acid Bacteria from Goat’s Milk Potential Producer of Bacteriocin: Evidence from Liquid Chromatography-Mass Spectrometry

The diverse microbial populations in milk produce a range of antimicrobial compounds that confer preservative action. Goat milk characterized by high nutritional value, medicinal properties and hypoallergenic in nature, constitutes the most prevalent non-bovine milk consumed globally. Lactic acid bacteria (LAB), renowned for their probiotic properties, are important constituents of goat milk microflora. In this study, bacterial strains with probiotic potential were isolated and characterized from milk samples of indigenous Indian goat breeds. On MRS medium, Gram-positive rods were observed after anaerobic culture. Based on 16s rRNA technique LAB from goat milk were identified to belong to Enterococcus durans and Lactobacuillus plantarum. Antimicrobial activities were observed against known pathogens (Staphylococcus aureus, Klebsiella pneumoniae, Escherichia. coli and Salmonella typhimurium) and minimum inhibitory concentration was found to be low (6.5 mg/ml) for most of the isolates. High resistance to both acidic condition (pH 2.0) and 0.3% bile salts was observed along with marginal increase in cell counts in some isolates. Adherence to Caco-2 cell lines was observed in all the four identified LABs and was higher in case of Enterococcus durans compared to Lactobacillus plantarum. LC-MS analysis revealed the presence of lacticin as one of the key component of cell free extracts (CFE) of selected isolate. Goat milk as a source of possible LAB probiotics opens up a whole new avenue of probiotics from non-bovine milk sources. LAB strains isolated in this study are potential probiotic candidates that can be employed as antimicrobial agents in food and pharmaceutical industries.

Heterogeneity and diversified distribution of αS2 casein variants in Indian goats

There is growing interest in goat milk and its derivatives, whose quality is essential in light of contemporary dietary trends favouring healthy eating. Goat milk is used in nutraceutical and infant food products for various reasons, including its hypoallergenic properties. Casein gene variation influences milk content and the chemical, physical, and technical aspects of goat milk. In Capra hircus, there are twelve variants of αs2 casein protein reported to date. The present study aimed to identify the polymorphism of alpha s2 casein and their transcript variants in six Indian goat breeds. Along with three reported alleles (A, B, and C), seven new alleles (L, M, N, O, P, Q, and R) were found in the six native Indian breeds. Transcript variants due to the exon skipping phenomenon were found. The novel alleles: N, P, Q, and R also represented the deletion of exon 3, 13, 6 and 6, respectively. The largest exon (exon 16) of the CSN1S2 gene was screened in 140 goats, and only one new allele, ‘S’, was found. Altogether, eight novel alleles were found in Indian goats along with two types of transcript variants.

Conservation priorities of Indian goat breeds based on genetic and non-genetic parameters

Indian goats have unique characteristics in terms of production, reproduction, disease resistance and adaptability in different agro-climatic regions of the country. Since, the country has vast goat genetic resources and different climatic regions but limited facilities including fund, there is a need for setting priority for conservation and better utilization. The microsatellite data of 1237 random DNA samples on 25 markers as well as morphological/ demographic information pertaining to 27 goat breeds/populations were used to study the extinction probability and conservation priority based on different approaches. Extinction probability based on census and microsatellite data revealed same order of priority for conservation in &gt;50% cases. Surti, Zalawadi and Gaddi were at higher risk of extinction probability (≥0.63) and more than half of the Indian goat breeds were having &lt;50% extinction probability. The study will help to manage goat genetic resources of the country and to conserve suitable breeds of goat.

Evaluation of candidate point mutation of Kisspeptin 1 gene associated with litter size in Indian Goat breeds and its effect on transcription factor binding sites

Kisspeptin gene (Kiss1) has a significant role in reproductive processes in mammals. However, only little information is available about the association of Kiss1 gene with litter size in Indian goat breeds. Thus, blood samples from 285 randomly selected animals were collected for DNA isolation and SNP profiling. The PCR product of 242 bp size harboring g.2540C>T mutation of Kiss1 gene was digested with the restriction enzyme Sac1. Least squares analysis revealed that Barbari goats showed significantly higher average litter size (2.86±0.08) compared to Beetal, Sirohi and Sojat breeds (P < 0.01). SNP locus g.2540C>T of Kiss1 gene also showed significant effect on litter size (P < 0.01). Goats with Genotype CT (2.66 ± 0.07) and TT (2.67 ± 0.26) had significantly higher (P < 0.01) litter size than CC (1.50 ± 0.05). From the transcription factor binding site analysis, it was predicted that due to g.2540C>T SNP, both native and mutant variant forms coded for putative binding sites for different transcription Factor. Allele T had putative binding sites for the androgen receptor which plays a significant role in the signaling pathway involved in increase in ovulation rate; which consequently can have a tremendous effect on average litter size.

Characterization of third exonic region of POU1F1 gene in the Osmanabadi breed of goat

The POU1F1 gene has been identified as one of the major gene for productivity, and its polymorphism is known to be associated with important production traits of various livestock. The present study was designed to investigate POU1F1 (exon-3) gene polymorphism and its association with body weight in Osmanabadi goat (n=217). The PCRSSCP and DNA sequencing revealed single ‘C’ &gt; ‘T’ transition at nucleotide position 42 in the third exonic region (225 bp) POU1F1 gene of Osmanabadi goat. Genotyping revealed ‘TT’ and ‘CC’ genotypes with predominance of ‘C’ allele in the Osmanabadi goat population. Though no association between the said SNP and body weight was observed, these findings can be extended to find the genetic variability of POU1F1 gene associated with growth traits of various Indian goat breeds.

Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India

The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats. A clear demarcation could be observed between the breeds in terms of expression of genes associated with lipid metabolism (FASN, SCD, THRSP, DGAT2 and FABP3). Most significant genes with high connectivity identified by gene co-expression network analysis were associated with triacylglycerol biosynthesis pathway in Barbari goat. Highly interactive genes identified in Changthangi goat were mainly associated with muscle fibre type. This study provides an insight into the differential expression of genes in longissimus thoracis muscles between Barbari and Changthangi goats that are adapted to and reared in different agro-climatic regions.

Semen quality and total microbial load: An association study in important Indian Goat breeds during different seasons.

The invasion of the male urogenital tract by microorganisms, and its subsequent effects on sperm fertilising ability, has not been well discussed in bucks. The present study was conducted to assess the bacterial load in fresh semen of the 2-6years old bucks. For conducting the experiment, semen ejaculates from 18 bucks (6 from each breed namely Jakhrana, Jamunapari and Barbari) were used. We collected 5 ejaculates from each buck in each season (Summer-April to June, Rainy-July to Sept and Winter-November to January). Semen was collected with the artificial vagina (AV) method, and separate AV was used for each buck every time. The semen collection frequency was once in a week. Immediately after initial evaluation, collected semen samples were transferred to the microbiology laboratory of the institute. Thereafter, the semen samples were subjected to bacteriological examination to assess the microbial load. The results of the current study indicate that the microbial load in the semen was significantly (p<0.05) higher in the Jamunapari bucks and in aged bucks. Bacteriospermia in different seasons was not significantly varied; however, nonsignificant increase in microbial load during the rainy season was observed. Overall, the average bacterial load in the semen of Jamunapari, Barbari and Jakhrana bucks was found 540.50±55.88CFU/ml, 391.81±46.33CFU/ml and 388.93±44.71CFU/ml respectively. No significant difference in bacterial counts in the subsequent ejaculates among bucks was observed. Moreover, correlation analysis revealed that the proportions of motility, viability, plasma membrane integrity and acrosomal integrity were negatively influenced by the increased bacterial contamination of buck semen.

Caprine MHC gene polymorphism and its association with endoparasitic infestation (Haemonchuscontortus) in Indian goat breeds

Caprine MHC gene polymorphism and its association with endoparasitic infestation (Haemonchuscontortus) in Indian goat breeds

Evaluation of Genetic Diversity at GDF9 and BMP4 Gene by Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) in Indian Goats

Genetic diversity of three Indian goat breeds namely Barbari, Sirohi and Black Bengal goats (Capra hircus) was evaluated using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method to detect polymorphism in two candidate genes (GDF9 and BMP4) in a sample of 90 goats with 30 goats of each breed. Both of the studied loci were polymorphic, having three variants for GDF9 and two variants for BMP4, in the studied population. Polymorphic information content (PIC) criterion revealed an intermediate polymorphism for all analysed phenotypic groups for Barbari, Sirohi and Black Bengal goats. Effective allele number criterion also revealed equally diverse nature of these genes. This preliminary study provides insight into the genetic diversity of Barbari, Sirohi and Black Bengal goats at GDF9 and BMP4 gene locus, which can be utilized for further study polymorphism and association of these polymorphic variants with traits of economic traits in future.

Genetic Diversity Analysis among 27 Indian Goat Populations using Microsatellite Markers

Background: Livestock genetic diversity studies focus on their within and diversity, breed history, adaptive variations, ancestral information, site of domestication and parentage testing and assess the genetic uniformity, admixture or subdivision, inbreeding, or introgression in the population which is helpful in breed formation and their sustainable utilization.Methods: The present research work was conducted during the year 2016-17 at National Bureau of Animal Genetics Resources, Karnal-132001. STR data of 25 markers on 1237 random samples of 27 goat populations was used for analysis. The genetic diversity analysis of new population viz: Narayanpatna, Raighar, Kalahandi, Malkangiri of Odisha state and Rohilkhandi (UK) and their association studies with other Indian goat breeds was performed.Result: It was found that used markers are highly polymorphic- and the studied breeds/population showed great diversity and distributed mostly on the basis of physio-geographical condition and type of production but among new populations diversity was least which might be due to exchange of animal for breeding purposes. The studied new goat populations were well differentiated from other goat breeds which might be due to physio-geographical condition and breeding practices, so these may be considered as separate breeds/populations. In conclusion, the results showed high level of conserved genetic diversity in the Indian goat breeds. The smaller and isolated new population showed less diversity and a higher inbreeding level as compared to registered breeds.