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Background: The goat population of Andhra Pradesh and Telangana states is about five million, respectively. The goats of these two states lack phenotypic uniformity. But it is not known whether these populations have any genetically uniform group that can be registered as a breed. The study was undertaken to explore possibility of any potential new goat germplasm. Methods: Study was carried out at ICAR-NBAGR during 2017-19. Genetic diversity and differentiation was evaluated by using 22 microsatellite markers in three goat populations: Telangana Black (TB, n=26), Telangana Mixed (TM, n=49) and one Andhra Pradesh goat population (AP, n=45). Their genetic differentiation was compared with that of geographically closely distributed registered breeds viz. Bidri (n=28) and Nandidurga (n=48) of Karnatka and Ganjam (n=48) of Odisha. Result: The mean allele frequency observed was 6.59 (TB), 7.27 (TM) and 8.36 (AP). Expected number of alleles varied from 3.33 in (TB) to 3.69 in AP goats. Observed heterozygosity was lowest in the TM (0.474) followed by TB (0.504) and was highest in the AP goats (0.569). AP goat population had 6.3% heterozygote deficiency, whereas, both TB (15.4%) and TM (17.5%) had very high inbreeding coefficients. A total of 344 alleles were detected across the 22 loci in six goat groups. F-statistics, the pair-wise Nei's genetic distance, assignment test and Baysian approach suggested that AP goats are distinct from two Telangana goat populations as well as from the other geographically closely related registered goat breeds. Genetic bottleneck analysis indicated the absence of any detectably large, recent genetic bottleneck in AP population. Altogether, the study identified Andhra Pradesh (AP) goats to be a new potential goat germplasm of India. [ABSTRACT FROM AUTHOR]

Black Bengal goats are an interesting genetic material to underpin the genetic mechanism of reproduction due to high prolificacy and sexual precocity. In the present study, novel SNPs in BMPR1B, BMP15 and GDF9 genes were genotyped to evaluate their association with the reproductive traits. PCR-RFLP and Tetra primer ARMS-PCR based protocols were developed for genotyping the six novel SNPs viz. T(-242)C in BMPR1B , G735A and C808G in BMP15 and C818T, A959C and G1189A in GDF9 . Linear mixed model for association of these SNPs with litter size and linear fix model for other traits were employed. The effect of season and parity was highly significant ( p ≤ 0.01) on litter size which varied with change in locus combination. However, there was no significant effect of genotype and year of birth on the litter size. Similarly, age at first heat, age at first service and age at first kidding were not affected by the year of birth as well as the genotype. Season of kidding did not affect the age at first heat and age at first service. However, significant ( p ≤ 0.05) association was observed between the season of kidding and the age at first kidding. The regression of age at sexual maturity on the age at first service and regression of age at first service on the age at first kidding was highly significant ( P ≤ 0.01). Further studies involving more number of breeds as well as animals may be fruitful for exploring the association of novel SNPs with caprine reproductive traits. [ABSTRACT FROM AUTHOR]

Reproductive traits are extremely important to the goat industry because moderate increase in litter size can lead to large profit. Traditional selection for improving litter size is difficult due to sex-limited nature and low heritability of the trait (5–10%). In addition, the lack of knowledge on the number of the genes controlling this trait and the possible gene interactions are the other limitations for this trait. Molecular genetics can overcome these limitations offering new opportunities for the improvement of reproductive traits, as it supplies tools to analyze genetic variability directly at the DNA level with the possibility of detecting the individual genes influencing the reproductive capability. For the last decade, molecular genetics has led to the discovery of individual genes or candidate genes with substantial effects on the reproductive trait viz. BMPR1B , GDF9 , BMP15 , FSHβ , FSHR , POU1F1 , PRLR , KiSS-1 , GPR54 , GH , INH , CART , GnRH , GnRHR , LHβ , BMP4 , KITLG , MT2 , CYP21 and AA-NAT . Despite the progress made in goat fecundity studies, it's hard to satisfy the actual application because the reproductive traits are complex quantitative traits involving multiple genes, loci and interactions. So it is important to analyze the combined effect of multiple genes or loci on reproductive traits. Little progress has been made on understanding interaction between genes, gene and environment, and genetic effect analysis. Thus the need of the hour is to identify more functional genes, clarify molecular mechanism of action and regulatory network and to resort to more holistic approaches like genomic selection which can tremendously accelerate the goat improvement. [ABSTRACT FROM AUTHOR]

KiSS1 is considered to be a key mediator of molecular mechanism of reproduction (puberty and prolificacy) in mammals. Kisspeptins are a family of structurally related peptides, encoded by KiSS1 gene, with ability to regulate gonadotropin-releasing hormone and hence hypothalamic–pituitary–gonadal axis. The present study investigated the polymorphism of caprine KiSS1 gene in 9 Indian goat breeds differing in sexual precocity and prolificacy. Comparison of KiSS1 amplified sequences of indigenous goats resulted in identification of nine SNPs (intron (1) G296C, T455G, T505A, T693C, T950C and intron (2) T1125C, A2510G, C2540T, A2803G) of which four are novel. These loci were not segregating together ( r 2 < 0.33). Mutations existed in both, sexually precocious and late-maturing goat breeds as well as low and high prolificacy goat breeds. Three loci reported to be associated with goat litter size (G296C, G2510A and C2540T) were identified in Indian goats as well. Association between loci of KiSS1 gene and age of puberty as well as litter size was explored in Black Bengal ( N = 158), a sexually precocious and prolific goat breed of India by designing PCR–RFLP. None of the mutations were found to be associated with reproductive traits however, difference in litter size as well age of sexual maturity for different genotypes indicates that the study on additional data based on more number of breeds and animals would be interesting to perform. Considering the importance of the reproductive trait in small ruminants, the results extend the limited information on genetic variation of the caprine KiSS1 , which might contribute toward molecular breeding to enhance productivity of goat. [ABSTRACT FROM AUTHOR]

Ladakh, one of the highest inhabited regions globally, hosts the unique Changthangi goat, renowned for producing Pashmina, the world's most luxurious natural fiber. In comparison, the fiber derived from Changthangi sheep is considered next only to Pashmina. This research endeavors to compare the skin transcriptome profiles of Changthangi goats and Changthangi sheep, aiming to discern the molecular determinants behind the recognition of Changthangi goats as the source of Pashmina. Drawing upon previously conducted studies, a collective of 225 genes correlated with fiber characteristics were extracted from the differentially expressed genes noticed between the two species (p-value of ≤ 0.05 and a log2 fold change of ≥ 1.5). These genes were analyzed using DAVID software to understand their biological functions and to identify enriched KEGG and Reactome pathways. The protein-protein interaction networks were constructed using Cytoscape, cytoHubba, and STRING to focus on key genes and infer their biological significance. Comparative transcriptome analysis revealed significantly higher expression of genes involved in signaling pathways like Wnt, MAPK, PI3K-Akt, Hedgehog, associated with fiber development and quality in Changthangi goats. These pathways play crucial roles in hair follicle (HF) formation, maintenance of epidermal stem cells, and fiber characteristics. Findings also highlight the enrichment of cell adhesion molecules and ECM-receptor interaction, emphasizing their roles in HF structure, growth, and signaling. This investigation offers an in-depth understanding of the molecular intricacies governing Pashmina production in Changthangi goats, providing valuable insights into their unique genetic makeup and underlying mechanisms influencing the exceptional quality of Pashmina fibers. [ABSTRACT FROM AUTHOR]

The detection of milk fat adulteration with foreign fats/oils continues to be a challenge for the dairy industry as well as food testing laboratories. Recently, various chromatographic methods have been developed to detect a low level of vegetable oil in ghee but detection of animal body fat in ghee is still a challenge. In India, goat body fat (goat tallow) adulteration in ghee is a very serious problem. In the present investigation, a rapid species specific polymerase chain reaction (PCR)-based methodology has been standardised to detect goat tallow in heat clarified milk fat (ghee). This standardised PCR-based protocol did not show any false positive results in the genuine ghee (heat clarified butter fat) samples. Adulteration of ghee (both cow and buffalo) with goat tallow at the 10% level could be detected using the standardised PCR-based protocol. The protocol standardised is rapid and convenient to use. [ABSTRACT FROM AUTHOR]

PRDM9 is the sole hybrid sterility gene identified so far in vertebrates. PRDM9 gene encodes a protein with an immensely variable zinc-finger (ZF) domain that determines the site of meiotic recombination hotspots genome-wide. In this study, the terminal ZF domain of PRDM9 on bovine chromosome 1 and its paralog on chromosome 22 were characterized in 225 samples from five ruminant species (cattle, yak, mithun, sheep and goat). We found extraordinary variation in the number of PRDM9 zinc fingers (6 to 12). We sequenced PRDM9 ZF encoding region from 15 individuals (carrying the same ZF number in both copies) and found 43 different ZF domain sequences. Ruminant zinc fingers of PRDM9 were found to be diversifying under positive selection and concerted evolution, specifically at positions involved in defining their DNA-binding specificity, consistent with the reports from other vertebrates such as mice, humans, equids and chimpanzees. ZF-encoding regions of the PRDM7, a paralog of PRDM9 on bovine chromosome 22 and on unknown chromosomes in other studied species were found to contain 84 base repeat units as in PRDM9, but there were multiple disruptive mutations after the first repeat unit. The diversity of the ZFs suggests that PRDM9 may activate recombination hotspots that are largely unique to each ruminant species. [ABSTRACT FROM AUTHOR]

Abstract: Genetic variation at 23 microsatellite loci, population structure, and genetic bottleneck hypothesis were examined for Jamunapari goat population found in Etawah, Uttar Pradesh, India. Estimates of genetic variability such as effective number of alleles and gene diversities revealed substantial genetic variation frequently displayed by microsatellite markers. Number of alleles observed across the microsatellite loci varied from 2 to 10 with an overall mean of 4.913±1.905. Average polymorphism across the studied loci and expected gene diversity in the population were 1.066±0.510 and 0.528±0.237, respectively. Population was observed to be significantly differentiated into different groups, and showed fairly high level of inbreeding (f =0.189±0.049) and global heterozygote deficit. Bottleneck analysis indicated the introduction of unique/rare alleles by immigrants. [Copyright &y& Elsevier]

• Genetic diversity was explored in 33 breeds/populations of Indian goats using mitochondrial DNA markers. • The haplotype and nucleotide diversity indices of Indian goats were 0.998 and 0.028, respectively. • Indian goats belong to four maternal haplogroups; A, B, C and D. • There was no genetic structuring of goats on the basis of geographical distribution. 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. [ABSTRACT FROM AUTHOR]