RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations

Kumar, Himansu; Choo, Hyo-Jun; Iskender, Asankadyr U.; Srikanth, Krishnamoorthy; Kim, Hana; Zhunushov, Asankadyr; Jang, Gul Won; Lim, Youngjo; Song, Ki-Duk; Park, Jong-Eun

doi:10.1038/s41598-020-76234-8

Cited by 10 publications

(5 citation statements)

References 39 publications

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“…Indeed, many pathways and metabolites had been found to be activated in order to maintain homeostasis and react to issues caused by oxidative stress. In more detail, glycogenolysis and gluconeogenesis (as also shown by Kumar et al [ 148 ]) as well as fat deposition, glycosylation, and glutathione production were increased. Finally, the transcriptome data have shown a trend to slow down the cell cycle in order to allow time for repairing DNA damage caused by HS [ 147 ] (Jastrebski et al, 2017).…”

Section: A Step Over Hspssupporting

confidence: 62%

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

Perini

Cendron

Rovelli

et al. 2020

Animals

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Chicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the past few decades and chicken meat is the main animal protein source in developing countries. Heat stress is one of the environmental factors which decreases the productive performance of poultry and meat quality. Heat stress produces the over-expression of heat shock factors and heat shock proteins in chicken tissues. Heat shock proteins regulate several molecular pathways in cells in response to stress conditions, changing the homeostasis of cells and tissues. These changes can affect the physiology of the tissue and hence the production ability of chickens. Indeed, commercial chicken strains can reach a high production level, but their body metabolism, being comparatively accelerated, has poor thermoregulation. In contrast, native backyard chickens are more adapted to the environments in which they live, with a robustness that allows them to survive and reproduce constantly. In the past few years, new molecular tools have been developed, such as RNA-Seq, Single Nucleotide Polymorphisms (SNPs), and bioinformatics approaches such as Genome-Wide Association Study (GWAS). Based on these genetic tools, many studies have detected the main pathways involved in cellular response mechanisms. In this context, it is necessary to clarify all the genetic and molecular mechanisms involved in heat stress response. Hence, this paper aims to review the ability of the new generation of genetic tools to clarify the molecular pathways associated with heat stress in chickens, offering new perspectives for the use of these findings in the animal breeding field.

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Section: A Step Over Hspssupporting

confidence: 62%

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

Perini

Cendron

Rovelli

et al. 2020

Animals

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“…RNA-Seq can help us to understand this question [ 15 ]. The study of different breeds of poultry from different geographical locations has been reported [ 16 ]. In this study, we implemented an RNA-Seq approach to compare transcriptome profiling of two chicken breeds.…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq Profiling between Commercial and Indigenous Iranian Chickens Highlights Differences in Innate Immune Gene Expression

Sadr

Nassiri

Ghaderi–Zefrehei

et al. 2023

Genes

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The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5). Overall, 1327 genes were significantly differentially expressed, of which 1013 genes were upregulated in the commercial versus the indigenous breed, while 314 were more highly expressed in the indigenous birds. Furthermore, our results demonstrated that the SPARC, ATP6V0D2, IL4I1, SMPDL3A, ADAM7, TMCC3, ULK2, MYO6, THG1L and IRG1 genes were the most significantly expressed genes in the commercial birds and the PAPPA, DUSP1, PSMD12, LHX8, IL8, TRPM2, GDAP1L1, FAM161A, ABCC2 and ASAH2 genes were the most significant in the indigenous chickens. Of notable finding in this study was that the high-level gene expressions of heat-shock proteins (HSPs) in the indigenous breeds could serve as a guideline for future genetic improvement. This study identified genes with breed-specific expression, and comparative transcriptome analysis helped understanding of the differences in underlying genetic mechanisms between commercial and local breeds. Therefore, the current results can be used to identify candidate genes for further breed improvement.

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“…In recent decades, studies of differentially expressed genes as a transcriptional response of the genome to various environmental stimuli or physiological/pathological conditions have been one of the most modern approaches (Gmoshinsky et al, 2018). The transcriptome of birds has previously been studied in connection with immunity (Wahl, et al, 2004), adaptive potential (Kumar et al, 2020) and meat productivity (Zhang, et al, 2021). However, experiments to study the effect of glyphosate on the transcriptome of living organisms have not been conducted before.…”

Section: Introductionmentioning

confidence: 99%

Studying the expression of productivity and immunity genes of chickens under the influence of feed glyphosate using the RNA-seq method

Laptev,

Yildirim,

Ilina

et al. 2023

BIO Web Conf.

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The aim of the study was to study the effect of different concentrations of glyphosate on meat productivity and differential expression of genes for immunity and broiler productivity. Broilers were divided into groups: Control I, who received a diet without the introduction of glyphosate, Experimental II, who received a diet with the addition of glyphosate at a dose of 10 mg/kg of feed (0.5 MPC for food); Experimental III, who received a diet with the addition of glyphosate at a dose of 20 mg/kg of feed (1 MPC); Experimental IV, who received a diet with the addition of glyphosate at a dose of 100 mg/kg of feed (5 MPC). Transcriptome analysis was performed by RNA-seq on the Illumina Miseq platform, using the TruSeq Stranded mRNA kit (Illumina, USA). In the 22-28-day period of broiler rearing, a decrease in live weight gain (83 g less) was observed in Experimental group III compared to Control I (P≤0.05). It has been shown that glyphosate at the level of 1 and 5 MPC for food causes activation (P≤0.05) of the proinflammatory response genes (IL15, IL1B, IL34, IL22) and apoptosis (Casp1, Casp2, Casp6, Casp7, Casp8, Casp9) up to 31.1 times, which probably leads to the redistribution of nutrients in in the body towards the immune system, reducing the functions of absorption in the intestine. In parallel, there is an inhibition (P≤0.05) of the expression of genes that have a direct effect on growth and development, which ultimately leads to a decrease in poultry meat productivity. Exposure to glyphosate is an important but unaccounted-for risk factor for reducing meat productivity in birds, acting through a change in gene expression.

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RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations

Cited by 10 publications

References 39 publications

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

RNA-Seq Profiling between Commercial and Indigenous Iranian Chickens Highlights Differences in Innate Immune Gene Expression

Studying the expression of productivity and immunity genes of chickens under the influence of feed glyphosate using the RNA-seq method

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