Rajwali Khan

NRF1 and ZSCAN10 bind to the promoter region of the SIX1 gene and their effects body measurements in Qinchuan cattle

The SIX1 homeobox gene belongs to the six homeodomain family and is widely thought to play a principal role in mediating of skeletal muscle development. In the present study, we determined that the bovine SIX1 gene was highly expressed in the longissimus thoracis and physiologically immature individuals. DNA sequencing of 428 individual Qinchuan cattle identified nine single nucleotide polymorphisms (SNPs) in the promoter region of the SIX1 gene. Using a series of 5′ deletion promoter plasmid luciferase reporter assays and 5′-rapid amplification of cDNA end analysis (RACE), two of these SNPs were found to be located in the proximal minimal promoter region −216/−28 relative to the transcriptional start site (TSS). Correlation analysis showed the combined haplotypes H1-H2 (-GG-GA-) was significantly greater in the body measurement traits (BMTs) than the others, which was consistent with the results showing that the transcriptional activity of Hap2 was higher than the others in Qinchuan cattle myoblast cells. Furthermore, the electrophoretic mobility shift assays (EMSA) and chromatin immunoprecipitation assay (ChIP) demonstrated that NRF1 and ZSCAN10 binding occurred in the promoter region of diplotypes H1-H2 to regulate SIX1 transcriptional activity. This information may be useful for molecular marker-assisted selection (MAS) in cattle breeding.

Association between FASN gene polymorphisms ultrasound carcass traits and intramuscular fat in Qinchuan cattle

Fatty acid synthase (FASN) is an enzyme involved with fat deposition and fatty acid composition in cattle. This study was conducted to detect single nucleotide polymorphisms (SNPs) of the FASN gene and explore their relationships with ultrasound carcass traits in order to assess the potential use of the FASN gene for the breeding selection of Qinchuan cattle for desirable carcass traits. The frequencies of SNP g.12740C>T, g.13192T>C and g.13232C>T were identified in 525 individual Qinchuan cattle which were also assessed for backfat depth, eye muscle area and intramuscular fat by ultrasound. According to the PIC values, g.13192T>C possessed an intermediate polymorphism (0.25<PIC<0.5). The SNPs of g.13232C>T, g.12740C>T possessed low polymorphism (PIC<0.25). Chi-square tests showed that g.13192T>C were in Hardy-Weinberg disequilibrium (c2<c0.052). Two SNPs were found to be associated with variation in ultrasound carcass traits. The H2H2 diplotypes had a greater back fat depth than H1H1, H1H4 and H1H2 (P<0.01). The TT genotype at g.13192T>C was associated with a greater eye muscle area and the TT genotype at g.13232C>T was associated with greater intramuscular fat. When these genotypes were combined there was no difference in eye muscle area and intramuscular fat between the diplotypes. The H2H2 diplotype was associated with carcass traits that are likely to provide economic advantage in Qinchuan cattle. Variations in the FASN genes and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.

Large low field magnetocaloric effect in first-order phase transition compound TlFe 3 Te 3 with low-level hysteresis

Magnetic refrigeration based on the magnetocaloric effect (MCE) is an environment-friendly, high-efficiency technology. It has been believed that a large MCE can be realized in the materials with a first-order magnetic transition (FOMT). Here, we found that TlFe3Te3 is a ferromagnetic metal with a first-order magnetic transition occurring at Curie temperature TCu2009=u2009220u2009K. The maximum values of magnetic entropy change (Δ) along the crystallographic c-axis, estimated from the magnetization data, reach to 5.9u2009J kg−1K−1 and 7.0u2009J kg−1 K−1 for the magnetic field changes, ΔHu2009=u20090–1u2009T and 0–2u2009T, respectively, which is significantly larger than that of MCE materials with a second-order magnetic transition (SOMT). Besides the large ΔSM, the low-level both thermal and field hysteresis make TlFe3Te3 compound an attractive candidate for magnetic refrigeration. Our findings should inspire the exploration of high performance new MCE materials.

KLF15 promotes transcription of KLF3 gene in bovine adipocytes

The Krüppel-like factors (KLF) family plays an important role in adipogenesis, which is subject to internal hierarchical regulation. KLF3 is a member of KLF family, mainly responsible for adipocyte differentiation and fat deposition. However, the transcriptional regulation of bovine KLF3 gene and its relationship with KLF15 gene remains unclear during bovine adipogenesis. Here, we report that the expression pattern of KLF3 and KLF15 genes during bovine adipogenesis, when KLF15 gene was overexpressed through adenoviral vector (Ad-KLF15) in bovine adipocytes the expression level of KLF3 gene was increased, similarly when KLF15 was down regulated through siRNA the expression level of KLF3 was also reduced. To explore the transcriptional regulation of bovine KLF3 gene and its relationship with KLF15, serial deletion constructs of the 5flanking region of bovine KLF3gene revealed through dual-luciferase reporter assay that the core promoter is located in -264 to -76 regions. The most proximal GGGG element in the promoter of the bovine KLF3 gene (located in -264 to -76 regions) is required for promotion by KLF15. Electrophoretic mobility shift (EMSA) and chromatin immunoprecipitation (ChIP) assays further confirmed that KLF15 gene binds to the KLF3 gene core promoter region in bovine adipocytes. These findings conclude that KLF15 promotes the transcriptional activity of KLF3 in bovine adipocytes. This mechanism to provides a new direction for further study of adipogenesis by internal regulation of members within KLF family.

Halal slaughtering, welfare, and empathy in farm animals: a review

Pre-slaughter and slaughter stressors are considered major concerns in animal welfare. Halal slaughtering method is considered one of the slaughtering stressors in livestock. This method seems to cause fear followed by stress in animals mainly due to inhuman handling. In this review, empathy and animal welfare are discussed in light of Islamic sharia and has further linked with animal’s physiology and behavioral responses during slaughtering. Islam as a religion forbids slaughtering an animal in front of another animal as through optic, olfactory, and cochlear senses animals can perceive the stress state of conspecifics. This suggests and strengthens the hypothesis that animals being slaughtered in front of each other may produce stress in them. This argument further leads to a claim that animals can experience empathy of each other through olfaction of semiochemicals (stress pheromones) emitted from animals slaughtered in the stressful condition that can be detected by other animals in abattoirs. Hence, research is needed to find out these specific stress pheromones and legislation needs to be adopted in slaughterhouses to isolate the areas of butchery from slaughtering lines to ensure proper guidelines of Halal slaughtering in slaughterhouses.

Genetic Variants in STAT3 Promoter Regions and Their Application in Molecular Breeding for Body Size Traits in Qinchuan Cattle

Signal transducer and activator of transcription 3 (STAT3) plays a critical role in leptin-mediated regulation of energy metabolism. This study investigated genetic variation in STAT3 promoter regions and verified their contribution to bovine body size traits. We first estimated the degree of conservation in STAT3, followed by measurements of its mRNA expression during fetal and adult stages of Qinchuan cattle. We then sequenced the STAT3 promoter region to determine genetic variants and evaluate their association with body size traits. From fetus to adult, STAT3 expression increased significantly in muscle, fat, heart, liver, and spleen tissues (p < 0.01), but decreased in the intestine, lung, and rumen (p < 0.01). We identified and named five single nucleotide polymorphisms (SNPs): SNP1-304A>C, SNP2-285G>A, SNP3-209A>C, SNP4-203A>G, and SNP5-188T>C. These five mutations fell significantly outside the Hardy–Weinberg equilibrium (HWE) (Chi-squared test, p < 0.05) and significantly associated with body size traits (p < 0.05). Individuals with haplotype H3H3 (CC-GG-CC-GG-CC) were larger in body size than other haplotypes. Therefore, variations in the STAT3 gene promoter regions, most notably haplotype H3H3, may benefit marker-assisted breeding of Qinchuan cattle.

Transcriptional Regulation by CpG Sites Methylation in the Core Promoter Region of the Bovine SIX1 Gene: Roles of Histone H4 and E2F2

DNA methylation is a major epigenetic modification of the genome and has an essential role in muscle development. The SIX1 gene is thought to play a principal role in mediating skeletal muscle development. In the present study, we determined that bovine SIX1 expression levels were significantly higher in the fetal bovine group (FB) and in undifferentiated Qinchuan cattle muscle cells (QCMCs) than in the adult bovine group (AB) and in differentiated QCMCs. Moreover, a bisulfite sequencing polymerase chain reaction (BSP) analysis of DNA methylation levels showed that three CpG sites in the core promoter region (−216/−28) of the bovine SIX1 gene exhibited significantly higher DNA methylation levels in the AB and differentiated QCMCs groups. In addition, we found that DNA methylation of SIX1 core promoter in vitro obviously influences the promoter activities. An electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assay, in combination with site-directed mutation and siRNA interference, demonstrated that histone H4 and E2F2 bind to the −216/−28 region and play important roles in SIX1 methylation regulation during development. The results of this study provide the foundation for a better understanding of the regulation of bovine SIX1 expression via methylation and muscle developmental in beef cattle.

Genome-wide analysis reveals the effects of artificial selection on production and meat quality traits in Qinchuan cattle

A new strain of Qinchuan cattle (QNS) has been obtained after more than forty years of selective breeding, and it shows good performance and production traits. To characterize the genetic changes that have resulted from breeding, we sequenced 10 QNS and 10 of the original breed Qinchuan cattle (QCC) for the first time, with average of 12.5-fold depth. A total of 31,242,284 and 29,612,517 SNPs were identified in the QCC and QNS genomes, 47.81% and 44.36% of which were found to be novel, respectively. Furthermore, population structure analysis revealed the selection that these cattle had experienced. Then, 332 and 571 potential selected genes were obtained, associated with enhanced immunity and acclimatization in QCC (CD5, SMARCA2, CATHL2, etc.) and production or meat quality traits in QNS (PLCD3, MB, PPARGC1A, etc.). These results revealed the efforts of selective breeding for Chinese Qinchuan cattle, and will be helpful for future cattle breeding.

Polymorphism in promoter of SIX4 gene shows association with its transcription and body measurement traits in Qinchuan cattle

The sine oculis homeobox homolog 4 (SIX4) gene belongs to the SIX gene family, which plays a critical role in muscle regeneration and early stages of ontogeny. This study aimed to detect promoter variations of bovine SIX4 genes in Qinchuan cattle, and to evaluate the effect of transcription regulations and body measurement traits. Quantitative real-time PCR (qPCR) results showed that the mRNA expression levels of SIX4 gene were found significantly highest in longissimus thoracis tissue and individual before attaining the stage of physiological maturity. Using sequencing technology on a total of 428 Qinchuan cattle, seven single nucleotide polymorphisms (SNPs) were identified in the promoter region of SIX4, and seven haplotypes representing 18 potential transcription factor compositions of polymorphic potential cis-acting elements. Association analysis indicated that the H3-H3 diplotype performed greater withers height, chest depth, chest circumference, back fat thickness and ultrasound loin muscle area (Pu202f<u202f0.05) than H5-H6, which were consistent with the promoter activity of Hap3 haplotype was higher than the Hap5 and Hap6 haplotype in vitro. These potential transcription factor information and combined genotypes H3-H3 of the SIX4 gene can be used as a molecular marker for selection of economic traits in Qinchuan cattle.

Genetic variants in the promoter region of the KLF3 gene associated with fat deposition in Qinchuan cattle

Krüppel-like factor 3 (KLF3), a member of the Krüppel-like factor (KLF) family, plays an important role in adipogenesis and lipid metabolism. The aim of this study was to investigate whether KLF3 could be used as a candidate gene in the breeding of cattle. The expression pattern of bovine KLF3 gene revealed that it was highly expressed in abdominal fat and perirenal fat. Using DNA sequencing, three single nucleotide polymorphisms (SNPs) within the promoter regions of KLF3 gene were identified in 448 Qinchuan cattle, which are located in the recognition sequences of 11 transcription factors and the four haplotypes representing four potential different compositions of polymorphic potential cis-acting elements. Association analysis results indicated that individuals with the Hap7/7 diplotype showed higher (Pu202f<u202f0.05) intramuscular fat content (IFC) than those with H7/8. In addition, the H7 haplotype had much higher (Pu202f<u202f0.05) transcriptional activity than the H8 haplotype, consistent with the association analysis. We speculated that polymorphisms in transcription factor binding sites of the KLF3 promoter region affected transcriptional activity of KLF3, which subsequently influence intramuscular fat content in Qinchuan cattle and KLF3 gene could be used as molecular markers for fat deposition traits using early marker-assisted selection (MAS) of Qinchuan cattle breeding in the future.