Indigenous Goats Research Articles

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat.

The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.

Comparative physico-chemical, texturural, colour and sensory characteristics of yogurt prepared from indigenous Goat and Cow milk

A study was conducted to compare the quality characteristics of yogurt of goat milk with cow milk. Yogurts of goat (GY) and Sahiwal (SY) and Hariana (HY) cow milk were prepared with 5.0% fat, 4.0% NCDC-144 (National Collection of Dairy Cultures) and 25% sugar. Moisture content was significantly P<0.05) higher in GY, whereas Brix values were significantly (P<0.05) higher in SY and HY. All textural characters (Firmness, consistency, cohesiveness and work of cohesiveness) were significantly (P<0.05) lower in GY than SY and HY. Lightness values were significantly (P<0.05) higher whereas yellowness values were significantly (P<0.05) lower in GY than SY and HY. Sensory characters (flavour, texture, sweetness and overall acceptability scores) were significantly (P<0.05) lower in GY than SY and HY. It was concluded that nutrient contents of yogurt of goat milk was similar to indigenous cow milk; however, overall acceptability of yogurt of goat milk was comparatively lower than indigenous cow milk.

Morphometric and morphological analysis of indigenous Matabele goats of Zimbabwe

This study aimed to characterize Matabele goats based on their qualitative and quantitative traits, to facilitate their genetic improvement and conservation. Data were collected from 120 goats over 12 months, comprising 20 males and 100 females using a stratified random sampling approach. Body weight and various body measurements were recorded. Five growth curve estimation models were employed to describe the growth pattern of Matabele goats. Descriptive statistics were computed for both qualitative and quantitative traits. T-tests were conducted to assess the impact of sex on morphometric measurements in different age groups. The results revealed an average body weight of 20.93 kg, with significant sex-related differences (p &lt; 0.05) observed across all quantitative traits. Most goats displayed horned and bearded characteristics, while black and white coat colours were predominant. Among the growth curve models, the Gompertz model exhibited the highest R2 value (0.992). Notably, the study found relatively low average morphometric measurements and body weight for Matabele goats, emphasizing the urgent need for genetic improvement efforts and the development of comprehensive breeding standards for this breed.

Detection of antimicrobial resistance genes in extended spectrum beta-lactamase-producing Escherichia coli from milk of indigenous Beetal goats of Punjab.

Antimicrobial resistance (AMR) is a burning issue in the present era. Mastitis in dairy animals is one of the most important causes of huge production loss to dairy farmers. Aims: The study aims to find the prevalence, antimicrobial resistance profile, and resistance genes in the extended-spectrum beta-lactamase-producing Escherichia coli in mastitic milk. A total of 125 milk samples were collected from Beetal goats suffering from clinical mastitis from different districts of Punjab and processed for bacterial isolation and further identification. The drug resistance profile of ESBL-producing E. coli and its associations with molecular markers was analyzed using statistical analysis. The prevalence of ESBL-producing E. coli in dairy goats of Punjab was recorded as 6.4%. The isolates showed the highest resistance to the beta-lactam group of antibiotics. The resistance percentages of streptomycin, gentamicin, tetracycline, chloramphenicol, clotrimazole, and colistin were 50%, 37.5%, 50%, 25%, 25%, and 50%, respectively. The isolates showed intermediate resistance to imipenem (12.5%) and tetracycline (25%). The ESBL-producing E. coli isolates harbored the resistance genes blaCTXM (100%), blaTEM (62.5%), blaSHV (25%), blaOXA (37.5%), tetA (37.5%), tetB (25%), aadA (37.5%), sul1 (25%), MOXM (12.5%), DHAM (25%), and blaCMY-2 (50%). Tetracycline and sulphonamide resistances were statistically associated with their respective resistance genes (P<0.05). Streptomycin resistance was not statistically associated with the presence of the aadA gene (P>0.05). The genes blaIMP and blaNDM were not recorded in any of the isolates. In this study, 12.5% of the isolates showed co-resistance to colistin and carbapenem. Antimicrobial resistance is a hot topic and requires immediate attention.

A 1.1 Mb duplication CNV on chromosome 17 contributes to skeletal muscle development in Boer goats.

The Boer goat is one of the top meat breeds in modern animal husbandry and has attracted widespread attention for its unique growth performance. However, the genetic basis of muscle development in the Boer goat remains obscure. In this study, we identified specific structural variants in the Boer goat based on genome-wide selection signals and analyzed the basis of the molecular heredity of related candidate genes in muscle development. A total of 9 959 autosomal copy number variations (CNVs) were identified through selection signal analysis in 127 goat genomes. Specifically, we confirmed that the highest signal CNV (HSV) was a chromosomal arrangement containing an approximately 1.11 Mb (CHIR17: 60062304-61171840 bp) duplicated fragment inserted in reverse orientation and a 5 362 bp deleted region (CHIR17:60145940-60151302 bp) with overlapping genes (e.g., ARHGAP10, NR3C2, EDNRA, PRMT9, and TMEM184C). The homozygous duplicated HSV genotype (+/+) was found in 96% of Boer goats but was not detected in Eurasian goats and was only detected in 4% of indigenous African goats. The expression network of three candidate genes ( ARHGAP10, NR3C2, and EDNRA) regulating dose transcription was constructed by RNA sequencing. Results indicated that these genes were involved in the proliferation and differentiation of skeletal muscle satellite cells (SMSCs) and their overexpression significantly increased the expression of SAA3. The HSV of the Boer goat contributed to superior skeletal muscle growth via the dose effects of overlapping genes.

Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate.

Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated whole-genome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient (Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia (SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex ( C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.

FLAVORED GOAT CHEESE AS A VALUE ADDED PRODUCT

Flavored goat cheese has huge potential in developing into a successful value added product. Goat cheese is a delicacy and could serve and cater to high value customers in the high end city restaurants, cafeteria and markets specialized for value added products. Goat cheese is healthier and neutraceutically enriched compared to conventional cow cheese. The benefits of goat cheese are high and this should be marketed as specialty products with health and nutritional benefits for the targeted customers. This could be an effective opportunity for small indigenous goat milk and cheese producers to supplement their annual income through on farm production of flavored goat cheese and allied products for their high value targeted customers.

Characterization of Indigenous Goat Husbandry Practices in Northwestern and Western Zones of Tigray Region, Ethiopia

Characterization of Indigenous Goat Husbandry Practices in Northwestern and Western Zones of Tigray Region, Ethiopia

Predicting the body weight of indigenous goat breeds from morphological measurements using the classification and regression tree (CART) data mining algorithm

Classification and regression tree (CART) is a tree-based data mining algorithm that develops a model to predict an outcome. This study purposed to create a model to predict the body weight (BWT) of Red Sokoto (RS), Sahel (SH), and West African Dwarf (WAD) goats using morphological measurements (such as body length, BL; head girth, HG; head width, HDW; face length, FAL; height at wither, HTW; rump length, RL; shoulder width, SW; rump width, RW; and rump height, RH). In total, 600 goats were used for this study (200 each of RS, SH, and WAD goats). Pearson?s Moment Correlation was used to evaluate the degree of association between BWT and each morphological measurement. Concomitantly, CART analysis was performed to estimate which independent variable (morphological measurements) played a considerable role in the BWT (dependent variable) prediction. In RS and WAD goats, a positive and statistically significant (p &lt; 0.0001) correlation was observed between BWT and each morphological measurement. However, in SH goats, both positive and negative statistically significant correlations were observed between BWT and morphological measurements. The CART analysis indicated that in RS and WAD goats, HG played a considerable role in BWT prediction, while, in SH goats, BL was considered the most critical independent variable in BWT prediction. Therefore, this study suggests that HG can be used as a prognostic index for BWT estimation in Red Sokoto and West African Dwarf, while BL can be used for Sahel goats. The SAS codes used are available via a GitHub repository (https://github.com/Soullevram/CART).

Quality Attributes of Suya from Indigenous Goat Breeds (Bucks) in Nigeria

A study was conducted to evaluate the percentage yield (%), proximate composition and organoleptic evaluation of the freshly prepared Suya product from indigenous goat (buck) breeds in Nigeria .Thigh muscle with average weights of 3.1±0.2 kg was excised from the carcasses of 9 fully matured bucks managed intensively for 90 days. The Chevon were dissected into smaller pieces of 10 cm long. The meat samples were thereafter trimmed of visible fats. They were also finely trimmed to very thin sheets of meat about 0.22 - 0.32 mm in thickness and with a length of about 4.5 cm - 9.3 cm. A total of 99 Suya sticks was prepared with 11 from each buck weighing approximately 88.50 g per stick. Suya ingredients used for the experiment were sourced from Bodija Market, Ibadan. The results showed that weight losses were considerable in all the treatments but the yield was not significantly different (P&gt;0.05) among the breeds. There was also no significant difference in moisture contents among the treatment groups while the protein, ether extract and crude fibre differed significantly across the treatments. Texture of Suya from Sahel bucks with 6.81±0.3 was significantly higher than 5.4±0.3 and 5.5±0.4 for WAD and Red Sokoto bucks respectively. The overall acceptability of Suya from Sahel bucks with 6.24 and Red Sokoto bucks with (6.9±0.1) were similar and most accepted than 5.10 of that from West African dwarf bucks.

GENETIC VARIATION AND PHYLOGENETIC RELATIONSHIPS BASED ON TESTIS DETERMINING REGION-Y (SRY) GENE IN THE LAKOR GOAT BREED

Lakor goat is an Indonesian indigenous goat breeds that successfully survive and is adaptive in the ecology of Lakor island in Southwest Maluku with high temperatures and curah limited rainfall. Genetic variations in Y-chromosome enable researchers to identify paternal lineages, which are informative for introgressions and migrations. This study aims to characterize genetic variation and phylogenetic relationships of Lakor goats based on male-specific region markers, i.e., sex-determining region-Y (SRY) gene. The genomes of 84 follicle samples of male goats (bucks) collected from Lakor island, were analyzed. The amplified product for SRY was 850 bp in encoding region (exon-1). Genetic variation and paternal phylogenetic relationship were established following sequencing using MEGA version X.0 software. The results of Y-chromosome alignments of the entire sequences identified two polymorphic nucleotides between individual goats within the population. Two polymorphism nucleotides, i.e. site 362 (A-G), and found in LK3, LK7, LK11, and LK13 samples, while site 410 (C-T) was found in LK3, LK7, LK11, LK13, and LK24 samples. The two mutations are categorized as substitution (transition type) and this is in the exon-1 area. This study concluded that genetic variation is very low in the Lakor goat breed and phylogenetic analysis grouping is a single clade or monophyletic group.

Assessment of Genetic Diversity and Conservation in South African Indigenous Goat Ecotypes: A Review.

Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization.

Correlation of Certain Biochemical Constituents of Seminal Plasma with Semen Characteristics in Pantja Buck

Background: Pantja is a dual purpose indigenous goat breed, reared in Tarai region of Uttarakhand and Uttar Pradesh. There is a lack of thorough study about the seminal characteristics of this goat breed. Hence, the present study was conducted to evaluate the level of certain biochemical constituents and their relationship with macroscopical and microscopical semen characteristics in Pantja buck. Methods: A total thirty two ejaculates from four sexually mature Pantja buck were analysed. The ejaculates were evaluated for volume (0.36±0.06 ml), mass activity (4.47±0.22), concentration (3.54±0.13 x 109/ml), individual motility (85.28±1.17%), viability (88.28±0.78%), morphological abnormalities (4.70±0.17%), plasma membrane integrity (86.31±0.62%) and acrosome integrity (94.31±1.05%) by standard semen evaluation protocol. Seminal plasma ALT (18.10±0.45 U/L), AST (124.04±0.86 U/L), ALP (49.98±0.38 U/L), LDH (216.36±1.78 U/L), GSH-Px (10.90±0.21 U/ml), MDA (2.14±0.05 nmol/ml), albumin (2.29±0.03 gm/dl), globulin (2.52±0.02 gm/dl), total proteins (4.81±0.05 gm/dl), calcium (11.07±0.18 mg/dl) and phosphorus (12.34±0.20 mg/dl) were determined spectrophotometrically. Two tailed Pearson’s correlation was applied to check the relationship among the above attributes. Result: A significant correlation was observed among the biochemical constituents of seminal plasma and seminal attributes of Pantja bucks. The selected biochemical constituents also showed significant correlation with each other.

Detection of small sequence variations within the goat GHR gene and its effects on growth traits

Growth hormone receptor (GHR) gene is considered to be an important candidate gene in growth traits. Therefore, the purpose of this study was to detect whether there were potential indel variations in the GHR gene that were related to the growth traits of the Shaanbei white cashmere goats (SBWC). In this study, genomic DNA from 931 healthy SBWC individuals were used to verify the relationship between the indel of the GHR gene and growth traits. Two indel variants, P49-bp indel in intron 1 and P1410-bp indel in 3’-UTR, were confirmed. Association analyses demonstrated that these two indel polymorphism loci were associated with the chest circumference and chest width of SBWC. Additionally, for the P49-bp and P1410-bp indel loci, the ID and II genotypes were dominant genotypes, respectively. Moreover, the genotypic distributions of these two indel loci in SBWC were significantly different from those in three other Chinese indigenous goat breeds (HNBG, GZDG and IMWC) (p < 0.05). Taken together, two indel loci (P49-bp indel and P1410-bp indel) both significantly affected the growth traits of goats. This illustrated that these two indel loci might be the potential DNA marker for use in improving the selection and breeding of goats.

The whole mitochondrial genome signature of Teressa goat, an indigenous goat germplasm of Andaman and Nicobar Islands, India

The domestic goat is a livestock species of global importance due to its ability to adapt to different agro-climatic conditions. The present study deals with the mitogenome signature of Teressa goat, a registered goat germplasm of Andaman and Nicobar Islands. Teressa goat mitogenome was 16,640 bp in length with 13 protein coding genes (PCGs), 22 tRNAs, 2 rRNAs and a non-coding region. Among the protein coding genes, only ND6 was present on light strand (L), other genes were encoded by heavy strand (H). All the PCGs had either ATG or ATA start codon whereas incomplete stop codons were detected in ND1, ND2, COX3, ND3 and ND4. Haplogroup assignment indicated that Teressa goat falls under Haplogroup A, most prevalent goat haplogroup. Mitogenome based phylogenetic analysis revealed that Teressa goat shared close genetic affinity with Xiangdong black goat, Longdong black goat, and Jintang black goat of China and Jamnapari goat of Bangladesh. The results of the study will be helpful to understand the origin and migration route of the goat breed and for sketching conservation plan of the indigenous breed.

Body weight and linear body measurements of indigenous goat population in Awi Zone, Amhara region, Ethiopia

ABSTRACT The study was conducted with the objective of undertaking morphological characterization of indigenous goat population. A total of 640 goats were randomly selected from three districts and body weight and linear body measurements were recorded. All the quantitative traits were significantly (p < 0.05) affected by sex, age classes and agro-ecology except ear length and tail length. The lowland goat population had significantly higher body measurements than midland and highland goat population. The overall (LSM ± SE) of matured goat body weight, heart girth, and height at withers were 29.13 ± 0.22 kg, 71.24 ± 0.20 cm, and 66.61 ± 0.18 cm, respectively. The multiple regression analysis showed that heart girth explained more variation on body weight than any other linear body measurements. Therefore, body weight can be predicted using hearth girth with the equation y = −41.6 + 0.99x for does and y = −44.3 + 1.10x for bucks.

Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

Simple SummaryJianchang Black goats are one of the indigenous black goat breeds in China. They are known for their crude feed tolerance but have a low growth rate and small body size. However, little is known about the genetic composition of Jianchang Black goats. The purpose of this study was to systematically examine the genetic composition of this breed by conducting multiple population genetic analyses. Our results revealed that Jintang Black and Yunshang Black goats showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from Jianchang Black goats. Jianchang Black goats generally showed moderate inbreeding levels. Importantly, we identified several putatively selected genes that may be potentially related to immunity, behavior, and reproduction in this breed. The current study provides valuable references and genomic resources for the future breeding of Jianchang Black goats.Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.

A study on the productivity and mortality rates of native and blended goats in Dodoma, Tanzania

The focus of breeding animals such as goats has been to increase productivity and other benefits from domestic animals. A breeding programme for producing blended goats is ongoing in Mpwapwa, Dodoma, Tanzania. However, few studies have been conducted to understand the performance of the produced breed (blended goat) in comparison with local indigenous goats. This study assessed the performance of blended and local indigenous goats in terms of milk and meat productivity while taking into consideration birth type, mortality rate, diseases causing mortality, and management system used. Primary and secondary data collection methods were used in this study. The weight, length, and girth of 2-year-old kids were measured in the morning and evening, and milk production in a lactating doe was recorded. Secondary data on the weight, length, and girth of inborn between 2010 and 2020. The results showed significantly higher productivity for blended goats than for indigenous goats in terms of meat and milk production (P < 0.005). The mortality rate of indigenous goats was not significantly higher than that of blended goats (P > 0.05). Diseases significantly influence goat mortality. Breed, management system, and milking time had a significant impact on goat productivity. For instance, morning milking produced significantly more milk than evening milking (P < 0.05). It is conclusive that the blended goat performs better than the indigenous goats in terms of milk and meat productivity. We recommend and encourage the adoption of blended goats by farmers who want to maximize goat production while considering other factors such as milking time, disease intervention, and management system used.

Differential gene expression and identification of growth-related genes in the pituitary gland of South African goats

Growth and carcass quality are economically important traits in goat production. This study investigated differentially expressed genes from the caprine pituitary gland transcriptome of South African indigenous goat breeds of varying growth performances and carcass quality parameters. Tissues were harvested from the pituitary gland of three South African Boer goats and three village ecotype goats all raised under similar conditions simulating intensive commercial production systems. Three additional tissues were harvested from village ecotype goats that were raised extensively on village farms. Between breed differences were investigated by comparing differential gene expression among three South African Boer and three village goats that were both raised under intensive commercial production system at a research farm. Within-breed differences were investigated by comparing differential gene expression among three village goats raised under extensive conditions (on-farm in Pella, S.A. village farming community) and three village goats raised under intensive commercial production system (at ARC research farm in Pretoria, South Africa. Total RNA was isolated from the pituitary gland of 36-week-old animals (n = 9) and sequenced individually in triplicates. An average of 28,298,512 trimmed, and quality-controlled reads/animal were mapped to the goat genome (Capra_hircus.ARS1.94) using HiSat2 software. Transcript assembly and quantification yielded 104 differentially expressed genes for village goats raised under extensive system and 62 for village goats raised under the intensive production system at the false discovery rate (FRD) of ≤0.05 and a fold change of ≥2. Growth-related genes such as POU3F4 and TSHZ1 were highly expressed within breeds raised under both production systems. Conversely, growth-related genes such as FGFR2 and SMPX genes were highly expressed between breeds raised under similar production systems. Ballgown analysis revealed a high expression of GH1 and IGF1 in the intensively raised compared to extensively raised goats. Both genes were also highly expressed in the village goats when compared to the Boer. The differential gene expression data provided insights into genes and molecular mechanisms associated with growth and growth development in goats.

Evaluation of growth curve for South African non-descript indigenous goats using non-linear models

ABSTRACT Six non-linear regression models (3P and 4P Gompertz, 3P, 4P and 5P Logistic and Neural network) were computed to construct the growth curves of 50 South African non-descript indigenous goats (males = 20 and female = 30) from birth to twelve months of age, raised at the University of Limpopo Experimental Farm, South Africa. Candidate non-linear models were compared for the best predictive values based on the adjusted coefficient of determination (AdjR 2), root mean square error (RMSE), Akaike’s information criterion (AIC) and Bayesian information criterion (BIC). The results suggest that South African non-descript indigenous goats’ growth curve was best reconstructed in males using Logistic 4P, while Logistic 5P for the females. The growth parameters obtained from the current study might be used to define the feeding programmes to meet nutritional needs of South African non-descript indigenous goats from birth to one year of age.