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Cattle belonging to seven different genetic groups in Kerala state, India were chosen for the study to find out the genetic diversity between the groups, which would aid in their sustainable improvement and conservation of native cattle. They included the native groups namely, Vechur, Kasaragod, Vadakara dwarf and Vilwadri, along with three different grades of crossbred cattle, based on milk production. Genomic DNA was isolated from 20 to 30 unrelated animals of each group and a panel of 25 microsatellite markers as suggested by FAO-ISAG, were amplified by multiplex PCR. The PCR amplicons were genotyped and the allelic data analyzed using suitable Bioinformatics softwares. The present study showed that the observed number of alleles was much more than the expected, in all populations. The mean PIC value obtained for the present study was 0.8912 and increased number of private alleles were observed, especially in Vilwadri and Kasaragod groups. Negative value of FIS (−0.055) indicated that the level of inbreeding was less. The FST value was 0.1442 indicating that the populations showed good genetic differentiation. The results of Structure analysis revealed admixture only in Vadakara population. The results obtained from the present study showed that Vilwadri and Kasaragod cattle showed distinct differences from other groups. [ABSTRACT FROM AUTHOR]

The legendary Vechur cattle of Kerala, described as a very short breed, and the crossbred (CB) Sunandini cattle population exhibited great phenotypic variation; hence, the present study attempted to analyze the genetic diversity existing between them. A set of 14 polymorphic microsatellites were chosen from FAO-ISAG panel and amplified from genomic DNA isolated from blood samples of 30 Vechur and 64 unrelated crossbred cattle, using fluorescent labeled primers. Both populations revealed high genetic diversity as evidenced from high observed number of alleles, Polymorphic Information Content and expected heterozygosity. Observed heterozygosity was lesser (0.699) than expected (0.752) in Vechur population which was further supported by positive FISvalue of 0.1149, indicating slight level of inbreeding in Vechur population. Overall, FSTvalue was 0.065, which means genetic differentiation between crossbred and Vechur population was 6.5%, indicating that the crossbred cattle must have differentiated into a definite population that is different from the indigenous Vechur cows. Structure analysis indicated that the two populations showed distinct differences, with two underlying clusters. The present study supports the separation between Taurine and Zebu cattle and throws light onto the genetic diversity and relationship between native Vechur and crossbred cattle populations in Kerala state. [ABSTRACT FROM PUBLISHER]

Toll like receptors play a key role in the innate immune system. These receptors are expressed in membrane compartments and on the cell surface of both immune cells like leukocytes and non-immune cells like epithelial cells and endothelial cells. The TLR genes, TLR2, TLR4 and TLR9 were involved in the recognition of pathogens and activation of innate immunity. TLR9 gene is particularly involved in the recognition of viral pathogens and thereby initiating antiviral responses. DNA isolated from blood sample of Vechur cattle well known for disease resistance was subjected to exome sequencing by next generation sequencing approach. Bioinformatics analysis of data by comparing with Bos taurus reference genome identified twenty SNPs (9 silent and 11 missense) in TLR2 gene, thirteen SNPs (11 silent and 2 missense) in TLR 4 gene and 2 silent SNPs in TLR9 gene. [ABSTRACT FROM AUTHOR]

Myogenin (MYOG) gene plays a significant role in regulating the number of skeletal muscle fibres, maintaining growth and homeostasis. The complete coding sequence of MYOG gene of Malabari and Attapady black goats were sequenced. The sequence analysis revealed a highly conserved nature of the gene across different species. [ABSTRACT FROM AUTHOR]

Background: Over many centuries, the conventional methods of poultry breeding is based on the phenotypic selection of the birds with superior trait in a particular population. Prolactin is a physiological candidate gene that has significant effects on production traits in poultry. The objective of this study was to investigate 24 bp insertion (I) polymorphism of prolactin gene and its association with quantitative traits in Tellicherry native chicken. Methods: A total of 200 blood samples were collected from the randomly selected birds of All India Co-ordinated Research Project (AICRP) on Poultry Breeding, Mannuthy. The isolated DNA samples were subjected to polymerase chain reaction (PCR) by using specific set of primers to amplify the 24 bp insertion polymorphism. PCR amplicons were sequenced to study the polymorphism at nucleotide level. Result: PCR amplification revealed the presence of a specific DNA fragment with 130/154 bp contained 24 bp insertion polymorphism. Based on the polymorphic patterns birds were designated with three genotypes as II, ID and DD. The frequency of I (0.6975) allele was found higher than D (0.3025) allele. Our experimental results revealed that 24 bp insertion polymorphism of prolactin did not have a significant association with production traits viz, age at sexual maturity, egg weight and egg number in Tellicherry native chicken. [ABSTRACT FROM AUTHOR]

The NAD+-dependent protein deacetylase, Sirtuin3 (SIRT3), plays a role in fertility by preventing the activation of reactive oxygen species (ROS). A novel study was conducted on caprine SIRT3, to study its ovarian expression, explore the sequence variability in exon 7 and analyze its association with prolificacy in two native goat breeds of Kerala, Malabari and Attappady Black. The mRNA isolated from ovaries of six Malabari and Attappady Black goats were subjected to quantitative PCR (qPCR) using GAPDH and β-actin as reference genes. Genomic DNA was isolated from 185 goats (99 Malabari and 86 Attappady Black) and subjected to PCR-SSCP to identify polymorphism in exon 7 of SIRT3 and association with litter size was analyzed. The ovarian expression of caprine SIRT3 was significantly higher (p ≤ 0.01) in Malabari than low prolific Attappady Black. PCR-SSCP analysis revealed, exon 7 of SIRT3 was polymorphic with three genotypes namely, AA, AB and BB with a novel SNP, g.154C > T in the 3′UTR. A significant association (p ≤ 0.05) was noticed between the genotypes of SIRT3 and litter size. The results obtained from this study highlight the role of SIRT3 in reproduction and hence SIRT3 may be considered as a potential candidate gene for genetic improvement in goats. [ABSTRACT FROM AUTHOR]

Background: India is fortunate to have a vast livestock resource with the availability of 28 well defined goat breeds. Kerala is the home for two breeds of goats namely Malabari and Attapady Black. Due to high prolificacy and income through lower input goat rearing had attracted numerous farmers. Selection with the aid of molecular markers associated with production traits plays an essential role in goat breeding programmes. The EGR2 gene is a part of multigene family which encodes Cys2His2 type zinc-finger proteins which is responsible for DNA binding. This gene has a major role in cellular prolification, reproduction, proper growth and development ovarian follicles. Thus present study was conducted with an objective to detect single nucleotide variations of Early Growth Response 2 gene in native goat breeds of Kerala. Methods: This research was conducted in 153 Malabari goats and 129 Attappady Black goats from six centers viz., University Goat and Sheep farm Mannuthy and 5 field centers of ICAR-All India Coordinated Research Project on Goat Improvement. Genomic DNA was isolated and PCR was performed to amplify Exon 1, Exon 2 and 5 fragments of Exon 3 regions of Early Growth Response 2 gene. Single stranded conformation polymorphism (SSCP) technique was performed to detect Single Nucleotide Polymorphism (SNPs). Result: The SSCP revealed similar banding patterns and sequencing did not indicate any nucleotide variations in all the exons screened suggesting that EGR2 gene is highly conserved in native goat breeds of Kerala. This is the first study conducted to characterize EGR2 gene in goats making the current study a novel one. [ABSTRACT FROM AUTHOR]

Context: Two native goat breeds from Kerala, Malabari and Attappady Black, differ significantly in prolificacy (i.e. no. of kids born/kidding). Prolificacy is an important economic trait and the subject of genetic research showing that bone morphogenetic protein (BMP) genes have a significant effect. Double digest restriction-site associated DNA sequencing (ddRADseq) is a highly efficient and low cost technology for high density discovery of single nucleotide polymorphisms (SNPs), which could serve as predictive markers for animal breeding programs. Aims: The study was aimed at discovering SNPs in BMP genes that affect prolificacy, using ddRADseq followed by validation of selected SNP. Methods: Blood DNA samples of 10 highly prolific Malabari and 10 less prolific Attappady Black goats were pooled by group and subjected to ddRADseq. SNPs observed in BMP genes were investigated and compared between groups. A validation study was done for the c.614–32789C>T variant in 100 Malabari and 50 Attappady Black goats by using PCR-RFLP. Key results: In total, 6333 variants were identified by ddRADseq. Three variants were identified in BMP genes, which included two intronic variants c.614–32789C>T and c.490+6793T>C, in genes BMP6 and BMP5 and a downstream gene variant near the BMPR1B gene. According to ddRADseq data, variants in BMP5 and BMP6 differed in allelic distribution between Malabari and Attappady Black goats. For c.490+6793T>C in BMP5 , the CC genotype was predominant in the highly prolific Malabari whereas TC was present in the Attappady Black group. The variant c.614–32789C>T in BMP6 was genotyped as TC in Malabari and CC in Attappady Black goats by ddRADseq. This variant was predicted to have an effect on splicing, according to the tool SplicePort. On the basis of bioinformatics analysis and the role of BMP6 gene in follicular dynamics, the variant in BMP6 was selected for further validation studies. All three genotypes were identified by PCR-RFLP; the C allele was the rare allele in the population with an allele frequency of 0.36. Presence of both alleles C and T and the three genotypes CC, TC and TT in this larger population substantiated the robustness of ddRADseq technique. Conclusions: The technique discovered high confidence SNPs, which could be used for further validation and association studies to develop markers for selection of animals and for genetic improvement of this complex trait. Implications: Techniques such as ddRADseq provide a large number of SNPs, and investigation of those polymorphisms found across the genome will help to identify new loci affecting traits of interest. This, in turn, will aid in exploring genetically complex traits in a faster and cheaper manner. Single nucleotide polymorphisms (SNPs) are responsible for variations among individuals; therefore, reliable SNPs, if identified, could serve as predictive markers giving sound information about many productive/reproductive traits. Prolificacy is a complex trait in goats, and identification of high confidence SNPs linked with this trait is possible by ddRAD at low cost. Bone morphogenetic protein (BMP) genes plays a major role in reproduction, and in this study, SNPs were discovered from BMP genes, and a selected SNP was validated and could be used for further association studies. [ABSTRACT FROM AUTHOR]

We analyzed the effect of a single nucleotide polymorphism, g. C3141T in the 3′ UTR of Signal transducer and activator of transcription-1 gene (STAT1) on milk production traits in the Holstein Friesian crossbred cattle of Kerala (n = 144) by association analysis and expression study. The population was genotyped by restriction fragment length polymorphism using Pag1. Association study using the General Linear Model-Analysis of Variance revealed that none of the yield or composition traits analyzed were significantly differed. The expression profile of STAT1 gene in leucocytes of animals bearing homozygous genotypes was compared by quantitative real time PCR using SYBR green chemistry with and relative expression was not found to be significantly differed. The second stage of the study, the STAT1 mRNA spanning 3213 bp was amplified from leucocytes and sequenced (GenBank: MT459802.1). Two novel SNPs were identified; one synonymous mutation in the coding region (g.A1212G) and the other in the 3'UTR (g.T3042C). The novel SNPs might contribute to STAT1 gene regulation mediated by alternate spicing or binding sites for regulatory molecules. The results reiterate the importance of extensive studies of STAT1 gene variants to substantiate the presence of a quantitative trait loci for dairy traits in the vicinity of STAT1 gene. [ABSTRACT FROM AUTHOR]

Recognition of deleterious non-synonymous single nucleotide polymorphism (SNPs) aids in the assessment of genetic basis of diseases and prediction of clinical phenotypes. In this study, data obtained from whole exome sequencing of Vechur cow using Illumina HiSeq 2500 platform is compared with that of crossbred cattle of Kerala. Sequence analysis of selected 18 mastitis resistant genes, evaluated the consequence of non-synonymous SNPs in these genes from both Vechur and crossbred cattle of Kerala, using sequence and structure-based computational tools such as SIFT, PROVEAN and I-MUTANT 2.0. Compared to Vechur cattle, incidence of missense deleterious mutation to effect protein functioning were relatively higher in crossbred cattle. These results on the type of genetic variants and its impact on normal functioning of a protein will assist to predict and enhance the disease resistance in cattle breeds. [ABSTRACT FROM AUTHOR]

Background: Prolactin is a physiological candidate gene which has significant effects on egg production in poultry. Also, it plays a major role on incubation behaviour (broodiness) in birds. The main objective of the present study was identification of single nucleotide polymorphism (SNP) C-2161G in the promoter region of prolactin gene and its association with egg production in Tellicherry native chicken population. Methods: A total of 200 blood samples were collected from the randomly selected birds of Tellicherry native chicken in All India Co-ordinated Research Project on Poultry Improvement (AICRP) Farm, Mannuthy, Thrissur, Kerala. Isolation of Genomic DNA was done and the isolated samples were subjected to polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis to identify the SNP C-2161G of prolactin gene. Result: On the basis of RFLP patterns, birds were designated with three different genotypes namely CC, CG and GG. The allelic and genotypic frequency was calculated. The observed genotypic frequency at the SNP site C-2161G was CC (0.61), CG (0.160) and GG (0.23) and the frequency of allele was 0.69 for C and 0.31 for G. The egg production was shown to be statistically similar for the genotypes of SNP C-2161G. [ABSTRACT FROM AUTHOR]

Background: Dilated cardiomyopathy is the important myocardial disease and one of the most common cause of death in the medium to large size dog breeds worldwide. The disease is characterized by dilatation of cardiac chambers and thinning of walls leads to systolic failure. Mutations in some sarcomere genes leads to cardiomyopathy in humans. Sarcomere is an important multifunctional protein network involved in the signal reception and transduction. Mutations in ß-MYH7, MYBPC3 and TCAP genes produce alterations in the morphology of heart (hypertrophy or dilatation). Methods: In this study twenty apparently healthy and twenty five dogs with dilated cardiomyopathy (DCM) were selected from patients reported or referred to University Veterinary Hospital and Teaching Veterinary Clinical Complex, Mannuthy (2015-2017) based on the clinical examination, radiographic, electrocardiographic, haematobiochemical and echocardiographic studies cardiac disorders (Dilated cardiomyopathy and hypertrophic cardiomyopathy) were confirmed. Result: In the present study we investigated genetic alterations of exon 12 of ß-MYH7, 16 of MYBPC3 and 2 of TCAP gene in dogs by polymerase chain reaction -single stranded confirmation of polymorphism (PCR-SSCP). Polymerase chain reactions were analysed using acrylamide gel and samples with different pattern of bands were sequenced. Polymerase chain reaction-SSCP showed different migration of band pattern in the intron 1 of TCAP gene in one sample. [ABSTRACT FROM AUTHOR]

In the present study, ABCG2 gene of Vechur cattle of Kerala was sequenced and aligned using Basic Local Alignment Search Tool (BLAST) in National Centre for Biotechnology Information (NCBI) site. The results revealed that ABCG2 gene sequence of Vechur cattle shows 96% similarity with reference NCBI sequences. Addition of eleven base pairs in 13th intron in ABCG2 gene of Vechur cattle which derived a larger amplicon (303 bp) than expected (292 bp). A novel SNP (G4104A) was identified at 4104th position in intron 13 of ABCG2 gene of Vechur cattle. Further research is suggested to depict the association if any of the novel SNP and unique characters of Vechur cattle. [ABSTRACT FROM AUTHOR]

Background: The avian prolactin gene is highly conserved, located on chromosome number 2 and most sequence polymorphisms occurs in the 5? flanking region, 3? flanking region and the coding region of signal peptide. The present study was aimed at the identification of SNP C-2402T of prolactin gene and its association with production traits in White Leghorn chicken. Methods: A total of 200 birds of White Leghorn were selected from All India Co-ordinated Research Project on Poultry improvement (AICRP) farm, Mannuthy. Genomic DNA was isolated from venous blood. Polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis was done to identify the SNP C-2402T of prolactin gene. Result: All the birds were observed with the same genotype CC and the frequency of the C allele was one. [ABSTRACT FROM AUTHOR]

Aim: To analyze the promoter sequence of toll-like receptor (TLR) genes in Vechur cattle, an indigenous breed of Kerala with the sequence of Bos taurus and access the differences that could be attributed to innate immune responses against bovine mastitis. Materials and Methods: Blood samples were collected from Jugular vein of Vechur cattle, maintained at Vechur cattle conservation center of Kerala Veterinary and Animal Sciences University, using an acid-citrate-dextrose anticoagulant. The genomic DNA was extracted, and polymerase chain reaction was carried out to amplify the promoter region of TLRs. The amplified product of TLR2, 4, and 9 promoter regions was sequenced by Sanger enzymatic DNA sequencing technique. Results: The sequence of promoter region of TLR2 of Vechur cattle with the B. taurus sequence present in GenBank showed 98% similarity and revealed variants for four sequence motifs. The sequence of the promoter region of TLR4 of Vechur cattle revealed 99% similarity with that of B. taurus sequence but not reveals significant variant in motifregions. However, two heterozygous loci were observed from the chromatogram. Promoter sequence of TLR9 gene also showed 99% similarity to B. taurus sequence and revealed variants for four sequence motifs. Conclusion: The results of this study indicate that significant variation in the promoter of TLR2 and 9 genes in Vechur cattle breed and may potentially link the influence the innate immunity response against mastitis diseases. [ABSTRACT FROM AUTHOR]

Background: Broodiness is a sex linked behavioural trait observed in most of the domestic fowls and it's also known as incubation behaviour. Prolactin (PRL) is the principal gene which plays a crucial role to the onset and maintenance of broodiness in birds. The present study was aimed at identification of 24bp (insertion-deletion) indel polymorphism at the promoter region of prolactin gene and its association with broodiness in Telllicherry native chicken population. Methods: A total number of 200 birds of Tellicherry native chicken were randomly selected from All India Co-ordinated Research Project (AICRP) on poultry improvement, Mannuthy, Thrissur, Kerala. Blood samples were collected from the wing vein under aseptic condition and isolation of Genomic DNA was done. Isolated DNA samples were subjected to polymerase chain reaction (PCR) using specific set of forward and reverse primer to detect a 24bp indel polymorphism in the prolactin gene. PCR amplicons were subjected to further molecular analysis. Result: According to the polymorphic patterns birds were categorized to three different genotypes viz., II (insertion-insertion), ID (insertion-deletion) and DD (deletion-deletion). The genotype and allele frequency was calculated and the frequency of I allele (0.6975) was found to be higher than D allele (0.3025). Results of this study suggest that the incubation behaviour could be eliminated in Tellicherry native chicken population by increasing the frequency of I allele upon selective breeding which may enhance the egg production. Therefore, this 24bp indel polymorphism could be used as a molecular marker in poultry breeding. [ABSTRACT FROM AUTHOR]

Orbital asymmetry and the skeletal abnormalities associated with anophthalmos condition was studied using six each of hatched and unhatched chicks, using Toluidine Blue - Alizarin Red S staining of cartilage and bone protocol. Of these birds, one each of unilateral anophthalmos was also associated with beak deformities. Orbital part of the frontal bone, interorbital septum, horizontal plate of ethmoid bone and lacrimal bone were found defective in the affected side. Jugal bone was absent on the affected side and all these deformities collectively contributed to the deformed orbit. Etiology of these skeletal deformities and anophthalmos may be attributed to spontaneous and genetic aberrations, indicated by the mismatching between nucleotides at various locations in the ovomucoid gene. [ABSTRACT FROM AUTHOR]

Vechur is the world's smallest recognised cattle breed (Bos indicus) from Kerala, India. It has been included in the critically maintained breed category by Food and Agriculture Organization. To facilitate the ongoing conservation efforts and the faster multiplication of Vechur cattle, the conception rates (CR) of animals were studied with varying temperament. A total of 64 breeding animals aged between 2 to 12 years were selected and assessed for their temperament status using two temperament tests viz., Weighing-Temperament test (WT test) and Social Separation test (SS test). Animals were grouped into four categories viz., Docile, Restless, Nervous and Aggressive. The analysis was done by Univariate Analysis of Variance by using SPSS software. The mean conception rate was ranged from 62.07 to 78.36 for the various temperament classes based on WT test. In SS test, the mean conception rates ranged from 64.72 to 66.65 and there was no significant difference in conception rate of various categories based on both WT and SS test. It was noticed that the two extreme groups namely docile and aggressive groups numerically varied widely in the mean conception rates. Results of the study may be confirmed by future research using a large population and standardised temperament score. This would enable us to incorporate temperament as a trait of importance in the selection programmes for Vechur cattle. [ABSTRACT FROM AUTHOR]

The study was aimed at the identification of polymorphism in promoter region of prolactin gene using polymerase chain reaction (PCR) and find out their association with production traits in White Leghorn (IWN strain). A total of 200 birds of White Leghorn (IWN strain) which had under gone 28 generations of continuous selection were randomly selected from All India Co-ordinated Research Project (AICRP) on Poultry for eggs, Mannuthy. Blood samples were collected from all the birds and isolation of genomic DNA was done using DNA isolation kit. PCR was done to reveal the 24-bp insertion-deletion (indel) at the site of -358 in promoter region of prolactin gene and based on the polymorphic patterns, genotypes were designated as II, ID and DD. Out of 200 birds of White Leghorn 193 birds were observed with II genotype, 7 birds with II) genotype and no birds were rev ealed with DD genotype. The genotype frequencies of II, ID and DD were 0.965,0.035 and 0.000, respectively. As there was no DD genotype in the population, the birds with II and ID genotype alone were taken for further comparison with production traits viz., broodiness, age at sexual maturity (ASM), egg weight (EW) at 28, 32 and 40 weeks of age and egg number (EN) up to 40 weeks of age. These production traits did not have any significant association with the genotypes of 24-bp indel polymorphism. [ABSTRACT FROM AUTHOR]

An experiment was conducted using randomly selected 150 hens ofiWN strain of White Leghorn maintained at AICRP on Poultry Improvement, Mannuthy to identify the SNP in the exon 2 of ovocalyxin-32 gene and its association with the production traits. PCR-RFLP analysis was done to find the genotypes TT, TG and GG in exon 2. The genotypic frequencies of TT, TG and GG were 0.900, 0.047 and 0.053, respectively and the allelic frequencies of T and G were 0.92 and 0.08, respectively. The frequency of normal allele Twas much higher than the mutant G. The result of this study revealed no significant association of c.267T>G with body weight, egg weight, egg number, shell thickness and age at sexual maturity. Present study indicates that the SNP in the exon 2 of ovocalyxin-32 (OCX-32) can't be used as a marker for selection of IWN strain of White Leghorn for eggs. [ABSTRACT FROM AUTHOR]

Crosses of temperate cattle reared in tropical ambience lapse in heat tolerance, fertility and disease resistance. However, cross breeding zebu with high yielding exotic cattle seems necessary to meet the need for enhanced composite milk production per unit in view of food security. Thermal stress is considered as the main factor responsible for reduction of milk yield in tropical climate. Any model for the study of thermal stress in dairy cattle should encompass related effect of ambient parameters of temperature, humidity, wind speed and solar radiation as the stressor and behavioural, autonomic, neuroendocrine and immunological endpoints as responses. The responses reach different response states depending on the severity of the stressor. Response measurements are at behavioural, physiological, biochemical and cellular level, which also include hormone, protein and gene expression assays. By fitting these measurements to the described model we can work out the biological and economic cost of thermal stress and the level of adaptation of the dairy animal in question. Such studies taking in to consideration the diverse nature of climatic factors is imperative for finding ameliorative measures to reduce the thermal stress experienced by the existing cattle population and for the possible genetic and management strategies for evolving and maintaining a climatically adapted dairy stock in a state like Kerala. This review analyses suitable model for climatic adaptation studies in the hot and humid climate especially in small holder production systems. [ABSTRACT FROM AUTHOR]