Animal Gene最新文献

Heterochromatin in the genome plays a vital role in species differentiation and evolution. To characterize and unravel molecular composition of the heterochromatic regions of the genome in dipteran flies, especially in Sarcophagids, different banding techniques have been used previously which established the banding pattern of constitutive heterochromatin. The present study is an attempt to further explore the base specificity of rather highly condensed C-banded regions of chromosomes using restriction enzyme (RE) digestion along with Giemsa staining, in search of species-specific targets of RE digestion. Different REs such as Apa I, Cla I, Eco RI, Hind III, Hae III and Pvu II have been used to characterize the heterochromatic regions of two Sarcophaga species, i.e., Sarcophaga ruficornis and Sarcophaga argyrostoma. Some of the constitutively heterochromatic regions remain intensely stained indicating no targets for the enzyme cleavage, while some of the heterochromatic areas in both the species show remarkable and distinct digestion sites after the treatment of REs. In S. ruficornis, Hind III digests the entire autosomes including the pericentromeric regions and the sex chromosome; while Hae III and Pvu II selectively digest autosomes and sex chromosome. While in S. argyrostoma, Cla I digests the entire autosomes including the pericentromeric regions; Hind III and Hae III selectively digests autosomes and sex chromosomes. These findings suggest the presence of distinctive enzyme digestion targets on the heterochromatin, which may provide important evidence for the differential base specificity that were previously found to be constitutive in nature.

In ruminant species, endometrial remodeling plays a pivotal role in regulation of estrous cycle and establishment of pregnancy. Among interferon tau (IFNT) stimulated genes, cathepsin (CTS) L is one of them, which is up-regulated in the endometrium during early pregnancy and plays an important role in endometrial remodeling and embryo development. However, the specific role of CTSL is not yet documented in goats. Therefore, in the present study, coding sequence (CDS) of CTSL was cloned, characterized, and its temporal expression profile was also examined in the endometrium of caprine (cp) for the first time. A fragment of cpCTSL, 963 bp in length, was amplified from complementary DNA (cDNA) with a 936 bp coding sequence, which encodes a polypeptide of 312 amino acids. Coding and deduced amino acid sequences of cpCTSL exhibited 72.8 to 99.3% identities with other species. A polypeptide of 312 amino acids of cpCTSL revealed three domains, a signal peptide sequence, a pro-domain and a partially mature domain. Further, the relative expression of cpCTSL mRNA and protein was determined by quantitative real-time PCR and western blot, respectively, in the endometrium of pregnant and cyclic does. Both cpCTSL mRNA and protein were expressed maximally (P < 0.05) during early pregnancy and these were 11.34 and 5.48-fold greater (P < 0.05), respectively, as compared to cyclic does. It is concluded that CTSL is mostly similar in structure to other species and increased level in the endometrium indicates its involvement in endometrial remodeling to sustain pregnancy in goats.

Polymorphisms in the 5′ regulatory and translated regions of a heat shock protein 70 kDa protein –A1 (HSP70A1A) are observed as the responsible for cellular protection against heat stress and associated with heat tolerance in dairy cows. The present study was conducted to determine the genetic variation in the inducible heat shock protein 70–1 gene and its association with heat resistance in Chinese Holstein cattle. Three single nucleotide polymorphisms (SNPs) were newly identified in 149 multiparous lactating cows, using direct sequencing. Luciferase reporter assay method was conducted and showed that GG genotype in g.-133 (mutant) increased the promoter activity than did CC (wildtype). We performed DNAStar Protean Software to detect the hydrophilicity and secondary structure of the HSP70–1 protein. The results revealed the SNP in the coding region (g. 462 G/T) was found to bring changes to the amino acid sequence at 154 Gln → His. These results suggested that the genetic polymorphisms in the HSP70–1 gene may influence the heat resistance, and it can be used as a molecular marker in thermoregulation. Therefore, this study may prove beneficial of these markers in genetic selections for heat tolerance in Chinese Holstein.

Indigenous cattle breeds (Bos indicus) inhabited under diverse agroclimatic conditions may serve as a broad reservoir of genetic pool for identifying genes selected for local adaptation. The present study aimed at deciphering genomic diversity and identifying adaptation signatures of cattle breeds belonging to contrasting agro-climatic conditions: Siri and Ladakhi from cold hilly region; and Kankrej and Hallikar from hot arid and semi-arid regions, respectively. A total of 46 samples were genotyped using 777 K Illumina BovineHD BeadChip. The Principal Component Analysis brought together Hallikar and Kankrej, while Siri and Ladakhi formed a separate cluster. In contrast to the tropical cattle breeds, genetic variation was higher for temperate type. Linkage disequilibrium decay (r² < 0.2) in hot semi-arid/arid adapted (71–103 kb) and temperate-adapted (218–222 kb) breeds revealed that BovineHD BeadChip can be used in predicting their genomic breeding values. Runs of homozygosity and F_ST based selection signatures were also identified in these cattle breeds. Novel hypoxia-related genes viz. egl-9 family hypoxia inducible factor, hypoxia inducible factor 1 subunit alpha inhibitor and heme oxygenase 1 were detected in temperate adapted breeds, while heat stress (heat shock protein family H (Hsp110) member 1 and BAG cochaperone 2 and immunity (TANK binding kinase 1) related genes were identified in selection sweeps of tropical breeds. Gene ontology analysis identified several enriched terms for the genes in both hot semi-arid/arid and temperate adapted cattle breeds in ROH islands. The relevant adaptation signals found in the present study will help to establish new breeding opportunities with recognition of core genes.

The goal of the work reported herein was to investigate if a new methodology could provide gene expression profiles of brachiocephalicus muscle tissue from young steers and to compare this genetic expression with carcass traits determined at slaughter to identify potential candidate genes. Tissue samples were collected from steers using a fine needle biopsy from muscle in the neck region at weaning. Muscle tissue was removed using the Dunn Biopsy method, and RNA was extracted for sequencing and transcriptomic analysis. Animal groups for data analysis were designated using marbling score codes (MSC) established from carcass grade at slaughter, which identified DNER, PCBD1 and BGN genes associated with adipose; muscle genes included MAP7, PDE1B, and ADAMTS2; tenderness genes identified were FMO2 and ZKSCAN2; and marbling genes RPTN, DNER, and CACNA2D2. These results indicate muscle biopsies may yield complementary information associated with carcass traits to the current industry standards. Application of this technique may provide insight to the identification of candidate genes that could improve production decisions, increase accuracy of prediction from transcriptomic profiling, and ultimately speed genetic progress.

Silver pomfrets are spread along the Indo-West Pacific: from the Persian Gulf to Indonesia, Japan, West and Southwest of Korea and Eastern parts of China and forms a commercial fishery in all these countries. For formulating fishery management strategy of the silver pomfret, accurate population information is necessary. The genetic stock structure of silver pomfret in the Northern Indian Ocean was explored using 12 polymorphic microsatellite markers. Morphological and molecular studies confirmed that the silver pomfrets along the Northern Indian Ocean is Pampus candidus. Pampus candidus populations along Arabian Sea and Bay of Bengal region (F_ST = 0.049, P < 0.05) using microsatellite data revealed significant genetic differentiation which was further supported by multi-locus distance matrix testing (Principal Co-ordinate Analysis) and model-based clustering. The results indicate that there are three distinct genetic stocks of silver pomfret within the study area.

RNA sequencing (RNA-Seq) libraries are prepared by either selecting poly(A) messenger RNAs (mRNA-Seq) or by depleting total RNA of highly abundant ribosomal RNAs (total RNA-Seq). The ribosomal RNA (rRNA) depletion protocols offer an attractive option for novel transcript discovery, as they facilitate the simultaneous characterization of polyadenylated and non-polyadenylated RNAs, including non-coding RNAs. However, the cost associated with total RNA-Seq is much greater than that of mRNA-Seq. Hence, the determination of an optimal target sequencing depth for total RNA-Seq would assist researchers in optimizing the cost-effectiveness of their experiments. In this study, we evaluate the appropriate depth of sequencing needed for transcriptome profiling in total RNA-Seq using a random sampling method to generate varying levels of sequencing depth in three different porcine tissues. As expected, our results indicated that the depth of sequencing has the greatest effect on the identification and quantification of lowly expressed transcripts. We propose that a depth of 80 M reads per library is desirable to identify and quantify expression of transcripts across the genome. The protocol used in this study can be utilized to determine optimal sequencing depth in other tissues and/or species.

Fars native chicken (FNC) is utilized as a food source, and plays a critical role in earning money in rural areas. However, little attention has been paid to FNC at molecular level and its genetic background is unknown for organizing the breeding programs. For the first time, herein, the effect of Ovocalyxin-32 (OCX-32) variant on egg production traits was investigated. OCX-32 protein plays role in minerals deposition and completion of eggshell. 400 blood samples were collected and a 390-bp fragment including exon 3 in OCX-32 gene (c.193A > C) was amplified and genotyped using RFLP-PCR technique. The bioinformatics analysis showed that the studied SNP is messiness mutation and leads to the substitution of Histidine with Asparagine in protein structure. Two genotypes including AA and AC were identified and effect of genotypes on the age at first egg was significant. Phylogeny analysis indicated that the OCX-32 gene sequences of FNC and Coturnix japonica are genetically categorized into the same group. The gene network analysis showed that there was association among OCX-32 and other important candidate genes affecting body size, digestibility and egg proteins. Therefore, OCX-32 could contribute to overall egg production in chickens.

Prion diseases are a group of animal and human neurodegenerative, albeit transmissible diseases. The lack of effective preventive and therapeutic approaches represents a serious problem in their management. This is especially true for those prion diseases of animals which behave like infectious and contagious diseases. In the case of sheep scrapie, the well- known role of variations in the prion protein gene (PRNP) in conferring resistance/susceptibility represents an opportunity which has been exploited to select populations genetically resistant to the disease.

The recent description of Camel prion disease (CPrD) in Algeria and Tunisia and the suspicion falling into the category of infectious prion diseases, make urgent to investigate the possible existence of genetic determinants useful for its control.

Herein, we investigated PRNP variability in 232 animals from six dromedary populations (Azawad, Hybrid, Naili, Rguibi, Sahraoui, Targui) in Algeria. A Gly69Ser mutation was observed in a single animal of the Targui population and a Gly134Glu polymorphism in the Azawad, Hybrid and Rguibi populations, with a frequency of the 134Glu allele of 2.6%, 7.7% and 7.1%, respectively.

Although our work highlights a low variability of Algerian dromedary PRNP, as a possible indication of a recent evolutionary history of CPrD, it offers also evidence of PRNP variants whose role in prion disease resistance/susceptibility deserve to be deepened.

The micromolar calcium-activated neutral protease (CAPN1) gene encodes μ-calpain that degrades myofibril proteins under the post-mortem conditions which appears to be the primary enzyme in the postmortem tenderization process, hence affecting the meat quality. Objective of this study was to analyze genetic polymorphism of the CAPN1 gene in seven diverse Indian goat breeds. Direct DNA sequencing was carried out to identify the genetic polymorphisms in 84 unrelated goats representing seven different goat breeds (Barbari, Beetal, Ganjam, Sirohi, Black Bengal, Osmanabadi and Malabari). Six single nucleotide polymorphisms (SNPs) were identified in CAPN1 gene intron 17. The observed heterozygosity (Ho) was highest (0.50) in Sirohi and Osmanabadi (0.42) breeds and lowest in Black Bengal (0.06) breed. The expected heterozygosity (He) was highest (0.45) in Sirohi followed by Osmanabadi (0.37), Barbari (0.34) and Beetal (0.37). The allele frequencies ranged from 0.083 to 0.917 and the major allele frequencies ranged from 0.595 (locus 6499 T/C) to 0.917 (locus 6529 T/C). In Black Bengal, polymorphism at all theloci was fixed with the exception of 6417 T/G and 6533C/G. The identity values oscillated from 0.7866 to 0.9593. The Nei's genetic distances were below 0.0294. Genetic diversity among different goat meat breeds indicates possible role in meat quality trait. Allelic diversity at this locus could be used in further for the association between gene polymorphism and enzyme activity as well as caprine meat quality traits.