Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds.

The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.

Diagnosis of rabies using reverse-transcription polymerase chain reaction on post-mortem skin tissue specimens of the nasolabial plate in a rabies suspected cow: a case study.

In India, rabies in cattle is under-reported. Religious sentiments hamper its diagnosis, discouraging post-mortem examination, particularly opening the cranium. Specimens of peripheral tissue innervated by the cranial nerves could potentially be used as alternative diagnostic specimens to the brain. Herein, we present a case study of a novel approach for diagnosing rabies in a cow suspected of having rabies, using skin tissue specimens of the nasolabial plate obtained post-mortem. Brain and nasolabial tissue specimens tested positive for rabies using conventional reverse-transcription polymerase chain reaction. This approach has been previously shown to have a high diagnostic sensitivity in animals. We encourage further studies with more nasolabial plate skin specimens for both post- and antemortem diagnosis of rabies in cattle.

Identification and characterization of single nucleotide polymorphisms in DMRT3 gene in Indian horse (Equus caballus) and donkey (Equus asinus) populations.

Equines' ability in racing and riding as well as gaitedness have influenced the human civilization. Aim of this study was to identify and characterize the novel polymorphisms or SNPs in DMRT3 gene in Indian horse and donkey breeds. In this study, the DMRT3 gene was sequenced and characterized in 72 Indian horses' and 33 Indian donkeys' samples. One SNP (A > C) at 878 was found in studied horses while identical SNPs (A > C) at two different nucleotide positions i.e., 878 and 942 in DMRT3 gene (chromosome 23) were observed in studied Indian donkey breeds. Horses and donkeys both have a non-synonymous mutation (A > C) at nucleotide 878 (codon 61) that converts a Stop codon (TAG > TCG) to coding codon Serine, whereas donkeys have a synonymous mutation at nucleotide 942 (codon 82) that converts Serine (TCA > TCC) into Serine. A phylogenetic tree indicated that the DMRT3 gene was equally distributed among the equine breeds. Most of the donkey breeds have been shown high levels of genetic diversity while horse breeds and Halari donkey showed the least genetic diversity. Mutation in DMRT3 has a major impact on gaitedness in horses and is presented at a high frequency in gaited breeds and in horses breed for harness racing.

Effectiveness of Ethyl Acetate, 1-Octanol, and Soy Biodiesel in Stabilizing Ethanol-Diesel Fuel Blends and Performance of Compression Ignition Engine on Stabilized Fuel Blends.

A study was conducted to evaluate ethyl acetate, soy biodiesel, and 1-octanol as surfactants for stabilization of ethanol-diesel fuel blends. The evaluation was based on the temperature stability and engine performance of ethanol-diesel fuel blends stabilized by selected surfactants. Among the three selected surfactants, 1-octanol was most effective in stabilizing ethanol-diesel fuel blends. Out of 20 ethanol-diesel fuel blends prepared with 1-octanol as surfactant, only 3 blends showed distinct phase separation; the rest 17 remained stable in the entire temperature range of 0-45 °C. At the rated engine speed, eight ethanol-diesel fuel blends showed similar power-producing capability as that of diesel. The engine running on diesel developed a power of 3.71 kW, while the engine brake power with ethanol-diesel fuel blends was in the range of 3.67-3.74 kW at the rated load condition. The tested fuel blends resulted in slightly higher fuel consumption and increased emission of unburnt hydrocarbons as compared to the diesel fuel. The tested fuel blends had comparable thermal efficiency and acceptable UBHC and NO x emissions compared to diesel.

Genetic polymorphism in core promoter sequence of ACTRIIB gene and association analysis with growth traits in chicken.

Molecular breeding exploiting candidate genes is burgeoning reproductive approach to improve growth traits in poultry. The activin type IIB receptor (ACTRIIB) is a negative growth regulator, modulating action of many muscle growth regulators. PCR-single-strand conformation polymorphism was employed to unravel polymorphism in promoter region of the ACTRIIB gene and delineate its association with growth traits in Aseel and control broiler (CB). Analysis of 5' promoter region (1122bp) of ACTRIIB gene identified five SNPs, that is g. [56 G > C (SNP1), 352A > C (SNP2), 580G > A (SNP3), 625C > T (SNP4) and 962C > T (SNP5)] at SMAD, paired box 7 homeodomain binding motif, GC box and bHLH-PAS type transcription factors in CB and Aseel. CB had significantly higher body weight (BW) and average daily gain (ADG) at all SNP sites, except at SNP 1. The haplotype construction resulted 8 haplotypes in CB and Aseel population. The BW and ADG differed significantly (p < .05) at all ages in CB and Aseel. The diplotypes H1H8 and H1H4 manifested higher BW and ADG, while diplotypes H3H8 and H3H7 displayed BW and ADG at each age in both lines (p < .05). Aseel exhibited higher expression of ACTRIIB gene than CB by 70.17, 4.83, 1.41, 2.38, 5.13, 1.20, 2.90, 6.53 and 11.75 times for h1h2, h1h3, h1h4, h1h6, h1h7, h1h8 h3h4, h3h7 and h3h8, respectively. The H3H8 and H3H7 diplotypes exhibited higher level of mRNA and protein than H1H8 and H1H4. The regulatory upstream region of ACTRIIB gene demonstrates high degree of genetic diversity and can be harnessed as potential marker in genetic selection programmes for increasing meat production.

Molecular characterization and expression profiling of BMP 3 gene in broiler and layer chicken.

A study was carried out to characterize and explore the expression profile of BMP 3 gene in control broiler and control layer chicken. The total open reading frame of BMP 3 (1389 bp) was cloned and sequenced. The control broiler and control layer chicken showed variation at nucleotide and amino acid level with reference gene (Gallus gallus, NCBI Acc. No. NM_001034819). When compared to reference gene, the control broiler showed four nucleotide differences (c.192A>G, c.519C>T, 903G>A and 960C>G), while, control layer showed variation at c.33G>C, 192A>G, 858G>A, 904G>A, 960C>G and 1257C>T making six differences in total. However, between control broiler and control layer lines, nucleotide differences was observed at c.33G>C, 519T>C, 858G>A, 903A>G, 904G>A and 1257C>T. The change at amino acid level between reference and control broiler was p.D320N and with control layer chicken, it was p.D302N and p.D320N. On the other hand, a single amino acid difference (p.D302N) was observed between the control broiler and control layer chicken lines. The phylogenetic study displayed a close relationship between broiler and layer lines and reference gene and also with other avian species resulting in a cluster formation. These cluster in turn displayed a distant link with the mammalian species. The expression profile of BMP 3 gene exhibited a variation at different stages of embryonic development and also at post embryonic period among the lines with control layer showing higher expression than that of broiler chicken. The protein was also detected in bone marrow tissue of broiler and layer lines by western blotting. It is concluded that the BMP 3 gene sequence differed at nucleotide and amino acid level among the lines and the gene expressed differentially at different periods of embryonic development and also at post hatch period.

Single nucleotide polymorphism mining and nucleotide sequence analysis of Mx1 gene in exonic regions of Japanese quail.

AIM: An attempt has been made to study the Myxovirus resistant (Mx1) gene polymorphism in Japanese quail. MATERIALS AND METHODS: In the present, investigation four fragments viz. Fragment I of 185 bp (Exon 3 region), Fragment II of 148 bp (Exon 5 region), Fragment III of 161 bp (Exon 7 region), and Fragment IV of 176 bp (Exon 13 region) of Mx1 gene were amplified and screened for polymorphism by polymerase chain reaction-single-strand conformation polymorphism technique in 170 Japanese quail birds. RESULTS: Out of the four fragments, one fragment (Fragment II) was found to be polymorphic. Remaining three fragments (Fragment I, III, and IV) were found to be monomorphic which was confirmed by custom sequencing. Overall nucleotide sequence analysis of Mx1 gene of Japanese quail showed 100% homology with common quail and more than 80% homology with reported sequence of chicken breeds. CONCLUSION: The Mx1 gene is mostly conserved in Japanese quail. There is an urgent need of comprehensive analysis of other regions of Mx1 gene along with its possible association with the traits of economic importance in Japanese quail.