In silico Methods for Modeling of Genomic Regions for Immunological and Metabolic Gene Modulating to Stress Response in Chicken: Where We Are?

Publication history: Accepted - 30 April 2022; Published online - 1 September 2022Traditionally, commercial broilers are not well adapted and currently subjected to a variety of environmental challenges. In recent years, researchers have shown an increased interest in stress as one of the greatest environmental challenges to the profitability of sustainable intensive poultry production. In this scenario, understanding the complexity of the molecular basis and genomics of the stress response is critical to successful breeding programs for climate-adapted chickens. Recently, numerous popular studies have attempted to identify candidate genes that control stress responses in chickens. However, a number of questions regarding the choice of stress response remain unanswered or inadequately answered regarding the number of lead candidate genes that control components of the non-infectious and infectious stress response. With this motivation, 89 journal articles were collected for the primary investigation and those with low validity were excluded from further analysis. In short, we used three types of information sources, namely: text-based systematic review, in silico modeling, and both network and pathway approaches, to introduce more effective and bio-indicators of gene-controlling stress responses in chickens through older literature. Gene ontology (GO) and pathway networking of candidate gene associated with stress was loaded into Cytoscape for analysis. The result provides additional evidence and highlights, including nearly 9 candidate genes. According to published studies, CRYAB, HSP90AA1, IL6, HSPA2, HSF2, HSPB1, HSF3, PLK1, BAG3 are mostly associated with non-infectious and infectious stressors and may deserve further attention. String database analysis illustrated role of highlighted gene in multiple cellular task and functionally such as ATPase activity, cellular processes, including protection of the proteome from stress, folding and transport of newly synthesized polypeptides, activation of proteolysis of misfold proteins and the formation and dissociation of protein complexes. Obtained information from Animal QTL database indicated important role of chromosomes numbers 2, 3, 4, 5, 12, 14 and 24 associated with stress resistance and susceptibility. On this basis, this report attempts to find out whi

Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits.

Publication history: Accepted - 26 September 2022; Published online - 29 September 2022Simple Summary Cattle have the potential to seriously injure humans and cause damage to property. The risk of cattle reacting in a dangerous manner can be reduced through genetic selection for cattle which have a better temperament. A literature search was undertaken which returned papers which met the criteria of “Bovine”, “Genetics” and “Behaviour” or terms therein. Behavioural traits were grouped and their heritability, genomic associations and correlations with production traits examined. It was found that heritability estimates were more accurate in studies with large populations (n > 1000). Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible, suggesting that genetic improvement can be undertaken without negatively affecting production. There was variation between the results of the studies examined, and this underlines that any genetic study is population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required. Abstract People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be requiredThis research was funded by the Department of Agriculture, Environment and Rural Affairs (DAERA), Northern Ireland as part of the “TemperGene” project, grant number 19 1 03 (48283

De novo Transcriptome Assembly and Differential Expression Analysis of Catharanthus roseus in Response to Salicylic acid

Publication history: Accepted - 12 September 2022; Published online - 24 October 2022The anti-cancer vinblastine and vincristine alkaloids can only be naturally found in periwinkle (Catharanthus roseus). Both of these alkaloids' accumulations are known to be influenced by salicylic acid (SA). The transcriptome data to reveal the induction effect (s) of SA, however, seem restricted at this time. In this study, the de novo approach of transcriptome assembly was performed on the RNA-Sequencing (RNA-Seq) data in C. roseus. The outcome demonstrated that SA treatment boosted the expression of all the genes in the Terpenoid Indole Alkaloids (TIAs) pathway that produces the vinblastine and vincristine alkaloids. These outcomes supported the time-course measurements of vincristine alkaloid, the end product of the TIAs pathway, and demonstrated that SA spray had a positive impact on transcription and alkaloid synthesis. Additionally, the abundance of transcription factor families including bHLH, C3H, C2H2, MYB, MYB-related, AP2/ ERF, NAC, bZIP, and WRKY suggests a role for a variety of transcription families in response to the SA stimuli. Di-nucleotide and tri-nucleotide SSRs were the most prevalent SSR markers in microsatellite analyses, making up 39% and 34% of all SSR markers, respectively, out of the 77,192 total SSRs discovered

Human–Animal Interactions with Bos taurus Cattle and Their Impacts on On-Farm Safety: A Systematic Review

Publication history: Accepted - 17 March 2022; Published - 19 March 2022.Simple Summary: Cattle are large animals that can cause serious injuries to humans. Humans may encounter cattle through working on farms, living on a farm, or traversing fields with cattle. A systematic review was carried out to assess the factors which may lead to a dangerous interaction with cattle. A literature search was carried out to find papers that included the criteria ‘Bovine’, ‘Handling’, ‘Behaviour’ and ‘Safety’, or terms therein. The search returned 17 papers, and after collation, six themes were identified: actions of humans; human demographics, attitude, and experience; facilities and the environment; the animal involved; under-reporting and poor records; and mitigation of dangerous interactions. Exploration of these themes shows that more accurate recording of interactions before an injury is required. Furthermore, targeted, tailored education for anyone who may come into contact with cattle could reduce cattle-induced injuries. Abstract: Cattle production necessitates potentially dangerous human–animal interactions. Cattle are physically strong, large animals that can inflict injuries on humans accidentally or through aggressive behaviour. This study provides a systematic review of literature relating to farm management practices (including humans involved, facilities, and the individual animal) associated with cattle temperament and human’s on-farm safety. The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) was used to frame the review. Population, Exposure, and Outcomes (PEO) components of the research question are defined as “Bovine” (population), “Handling” (exposure), and outcomes of “Behaviour”, and “Safety”. The review included 17 papers and identified six main themes: actions of humans; human demographics, attitude, and experience; facilities and the environment; the animal involved; under-reporting and poor records; and mitigation of dangerous interactions. Cattle-related incidents were found to be underreported, with contradictory advice to prevent injury. The introduction of standardised reporting and recording of incidents to clearly identify the behaviours and facilities which increase injuries could inform policy to reduce injuries. Global differences in management systems and animal types mean that it would be impractical to impose global methods of best practice to reduce the chance of injury. Thus, any recommendations should be regionally specific, easily accessible, and practicable.Department of Agriculture, Environment and Rural Affairs (DAERA), Northern Ireland as part of the “TemperGene” project, grant number 19 1 03 (48283)

Single Nucleotide Polymorphism Effects on Lamb Fecal Egg Count Estimated Breeding Values in Progeny-Tested Katahdin Sires

Publication history: Accepted - 14 April 2022; Published - 3 May 2022.Estimated breeding values (EBV) for fecal egg counts (FEC) at 42–90 days of age (WFEC) and 91–150 days of age (PFEC) for 84 progeny-tested Katahdin sires were used to identify associations of deregressed EBV with single-nucleotide polymorphisms (SNP) using 388,000 SNP with minor-allele frequencies ≥0.10 on an Illumina high-density ovine array. Associations betweenmarkers and FEC EBVwere initially quantified by single-SNP linear regression. Effects of linkage disequilibrium (LD) were minimized by assigning SNP to 2,535 consecutive 1-Mb bins and focusing on the effect of the most significant SNP in each bin. Bonferroni correction was used to define bin-based (BB) genome- and chromosome-wide significance. Six bins on chromosome 5 achieved BB genome-wide significance for PFEC EBV, and three of those SNP achieved chromosome-wide significance after Bonferroni correction based on the 14,530 total SNP on chromosome 5. These bins were nested within 12 consecutive bins between 59 and 71 Mb on chromosome 5 that reached BB chromosome-wide significance. The largest SNP effects were at 63, 67, and 70Mb, with LD among these SNP of r2 ≤ 0.2. Regional heritability mapping (RHM) was then used to evaluate the ability of different genomic regions to account for additive variance in FEC EBV. Chromosome-level RHM indicated that one 500-SNP window between 65.9 and 69.9Mb accounted for significant variation in PFEC EBV. Five additional 500-SNP windows between 59.3 and 71.6 Mb reached suggestive (p < 0.10) significance for PFEC EBV. Although previous studies rarely identified markers for parasite resistance on chromosome 5, the IL12B gene at 68.5 Mbcodes for the p40 subunit of both interleukins 12 and 23. Other immunoregulatory genes are also located in this region of chromosome 5, providing opportunity for additive or associative effects.This research was funded by the USDA NIFA Organic Agriculture Research and Extension Initiative grants no. 2016- 51300-25723 and 2010-51300-21641, and USDA Southern SARE grant no. LS08-204

Genome-wide regional heritability mapping identifies a locus within the<i> TOX2</i> gene associated with Major Depressive Disorder

Background: Major depressive disorder (MDD) is the second largest cause of global disease burden. It has an estimated heritability of 37%, but published genome-wide association studies have so far identified few risk loci. Haplotype-block-based regional heritability mapping (HRHM) estimates the localized genetic variance explained by common variants within haplotype blocks, integrating the effects of multiple variants, and may be more powerful for identifying MDD-associated genomic regions. Methods: We applied HRHM to Generation Scotland: The Scottish Family Health Study, a large family- and population-based Scottish cohort (N = 19,896). Single-single nucleotide polymorphism (SNP) and haplotype-based association tests were used to localize the association signal within the regions identified by HRHM. Functional prediction was used to investigate the effect of MDD-associated SNPs within the regions. Results: A haplotype block across a 24-kb region within the TOX2 gene reached genome-wide significance in HRHM. Single-SNP- and haplotype-based association tests demonstrated that five of nine genotyped SNPs and two haplotypes within this block were significantly associated with MDD. The expression of TOX2 and a brain-specific long noncoding RNA RP1-269M15.3 in frontal cortex and nucleus accumbens basal ganglia, respectively, were significantly regulated by MDD-associated SNPs within this region. Both the regional heritability and single-SNP associations within this block were replicated in the UK–Ireland group of the most recent release of the Psychiatric Genomics Consortium (PGC), the PGC2–MDD (Major Depression Dataset). The SNP association was also replicated in a depressive symptom sample that shares some individuals with the PGC2–MDD. Conclusions: This study highlights the value of HRHM for MDD and provides an important target within TOX2 for further functional studies