RNA deep sequencing reveals novel transcripts and pathways involved in the unsaturated fatty acid metabolism in chicken

Gunawan, Asep; Listyarini, Kasita; Furqon, Ahmad; Jakaria, Md.; Sumantri, Cece; Akter, Syeda Hasina; Uddin, Muhammad Jasim

doi:10.1016/j.genrep.2019.100370

Cited by 4 publications

(5 citation statements)

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“…A member of APO gene family, APOV1 also known as APOVLDLII, is found to be down regulated in higher (UFA) sheep. This gene was previously reported to be associated with UFA in chicken [ 60 ]. Significant association between the variants in APOA5 gene and high triglyceride levels and FA composition have been previously documented in sheep [ 61 , 62 ].…”

Section: Discussionmentioning

confidence: 99%

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

et al. 2021

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Fatty acids (FA) in ruminants, especially unsaturated FA (USFA) have important impact in meat quality, nutritional value, and flavour quality of meat, and on consumer’s health. Identification of the genetic factors controlling the FA composition and metabolism is pivotal to select sheep that produce higher USFA and lower saturated (SFA) for the benefit of sheep industry and consumers. Therefore, this study was aimed to investigate the transcriptome profiling in the liver tissues collected from sheep with divergent USFA content in longissimus muscle using RNA deep-sequencing. From sheep (n = 100) population, liver tissues with higher (n = 3) and lower (n = 3) USFA content were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample were ranged from 21.28 to 28.51 million with a median of 23.90 million. Approximately, 198 genes were differentially regulated with significance level of p-adjusted value <0.05. Among them, 100 genes were up-regulated, and 98 were down-regulated (p<0.01, FC>1.5) in the higher USFA group. A large proportion of key genes involved in FA biosynthesis, adipogenesis, fat deposition, and lipid metabolism were identified, such as APOA5, SLC25A30, GFPT1, LEPR, TGFBR2, FABP7, GSTCD, and CYP17A. Pathway analysis revealed that glycosaminoglycan biosynthesis- keratan sulfate, adipokine signaling, galactose metabolism, endocrine and other factors-regulating calcium metabolism, mineral metabolism, and PPAR signaling pathway were playing important regulatory roles in FA metabolism. Importantly, polymorphism and association analyses showed that mutation in APOA5, CFHR5, TGFBR2 and LEPR genes could be potential markers for the FA composition in sheep. These polymorphisms and transcriptome networks controlling the FA variation could be used as genetic markers for FA composition-related traits improvement. However, functional validation is required to confirm the effect of these SNPs in other sheep population in order to incorporate them in the sheep breeding program.

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Section: Discussionmentioning

confidence: 99%

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

et al. 2021

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“…It should be emphasized that the glycerol obtained from hydrolysis of TG in VLDL cannot be re-used for esterifying fatty acids, so the adipose tissue acquires the glycerol 3-phosphate for TG resynthesized from pyruvate or glucose through gluconeogenesis and glycolysis, respectively [ 31 ]. Moreover, in egg-laying hens, the VLDL catabolism is very limited in adipose and muscle tissue, so a greater quantity of lipids is transported to the oocytes, which supply lipids for the production of the egg yolk [ 20 , 33 ]. Fat deposition in chicken depends on the TG availability in plasma, which is transported to adipocytes as a component of lipoproteins; therefore, we can say that chicken fattening is related to the three aspects of lipid metabolism, including lipid synthesis, lipid transport, and lipid utilization [ 34 ].…”

Section: Overview Of Lipid Metabolism In Chickenmentioning

confidence: 99%

“…Besides, it may play a potential role in controlling body weight and energy homeostasis in chickens [ 14 ]. The deep RNA-sequencing of chicken with divergent unsaturated fatty acid contents in the breast muscle indicated that SCD, which is located through the genomic region of a quantitative trait locus for intramuscular and abdominal fat, can be regarded as a positional and functional candidate gene for the regulation of unsaturated fatty acid metabolism in chickens [ 33 ].…”

Section: Important Genes Involved In Chicken Fat Metabolismmentioning

confidence: 99%

“…While, in the liver of peak laying hens, the expression of this gene was more significant, boosting lipid metabolism, TG, cholesterol, and VLDL biosynthesis in the liver. At the same time, RNA sequencing of chicken liver with divergent unsaturated fatty acid content showed that APOV1 along with SCD could be potential candidate genes involved in fatty acid metabolism in the chicken liver [ 33 ].…”

Section: Important Genes Involved In Chicken Fat Metabolismmentioning

confidence: 99%

“…There are several studies, investigating the main signaling pathways involved in lipid metabolism in chicken with divergent fat content, ages, and breeds. As an example, the RNA deep sequencing of liver from chicken with divergent unsaturated fatty acids content in their breast muscle revealed that the most dominant enriched pathways which have a significant role in unsaturated fatty acid metabolism were ECM-receptor interaction, focal adhesion, peroxisome, Wnt, and TGF-β signaling pathways [ 33 ]. On the other hand, the RNA sequencing of pectoralis muscle from broiler with divergent TG content revealed that key pathways controlling divergent lipid deposition and metabolism in chickens with high and low TG content were steroid biosynthesis (participating in cholesterol synthesis), PPAR signaling pathway, and cell junction-related pathways (focal adhesion, cell adhesion, tight junction, ECM-receptor interaction, regulation of actin cytoskeleton) [ 23 ] ( Figure 4 ).…”

Section: Main Signaling Pathways Involved In Chicken Fat Metabolismentioning

confidence: 99%

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Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken

Nematbakhsh

Chong

Selamat

et al. 2021

Genes

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In the poultry industry, excessive fat deposition is considered an undesirable factor, affecting feed efficiency, meat production cost, meat quality, and consumer’s health. Efforts to reduce fat deposition in economically important animals, such as chicken, can be made through different strategies; including genetic selection, feeding strategies, housing, and environmental strategies, as well as hormone supplementation. Recent investigations at the molecular level have revealed the significant role of the transcriptional and post-transcriptional regulatory networks and their interaction on modulating fat metabolism in chickens. At the transcriptional level, different transcription factors are known to regulate the expression of lipogenic and adipogenic genes through various signaling pathways, affecting chicken fat metabolism. Alternatively, at the post-transcriptional level, the regulatory mechanism of microRNAs (miRNAs) on lipid metabolism and deposition has added a promising dimension to understand the structural and functional regulatory mechanism of lipid metabolism in chicken. Therefore, this review focuses on the progress made in unraveling the molecular function of genes, transcription factors, and more notably significant miRNAs responsible for regulating adipogenesis, lipogenesis, and fat deposition in chicken. Moreover, a better understanding of the molecular regulation of lipid metabolism will give researchers novel insights to use functional molecular markers, such as miRNAs, for selection against excessive fat deposition to improve chicken production efficiency and meat quality.

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The genetic quality improvement of native and local chickens to increase production and meat quality in order to build the Indonesian chicken industry

Sumantri

Khaerunnisa

Gunawan

2020

IOP Conf. Ser.: Earth Environ. Sci.

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Native and local chickens have a great effect in the development of the local chicken industry in rural communities. Local chicken industry significantly contributes to the income value of national agricultural development as well as become an important foundation in building food self-sufficient. Indonesia has a wealth of genetic resources of native and local chicken with abundant genetic diversity, but has not been managed and utilized properly. In Indonesia, local chicken agribusiness is less developed due to lack of genetic improvement and has a direct impact with the very low contribution of meat and eggs. Indonesia has a variety of genetic sources for native and local chickens spread throughout the region. Native and local chickens contribute greatly to the rural economy but their production is still limited. Despite its low productivity, native chicken production is very important for rural communities. However, they face challenges how to increase the productivity of their population, which can benefit them financially and increase food security and reach market potential. This native chicken has the characteristics of slow growth and varied egg production. The development of the potential of native chicken and related issues of food security and food independence, local chicken is suitable for this. Information on the performance and productivity of local chickens is needed for local chicken development. Potential local chickens such as pelung chickens are known as singer chickens with a large body frame. Sentul chickens are another potential local chicken, known as meat-producing chickens with good egg production. Through breeding programs (selection and crossing), increasing the productivity of meat and eggs of native chicken can be done effectively. In addition, improving the quality of local chickens can be improved through conventional feeding management. The availability of selected local chicken in accordance to market demand is still limited. To overcome the lack of selected local chicken, the Faculty of Animal Science, IPB has been developing superior local chicken breed since 2012-2018 namely IPB-D1. The up-to-date Next Generation Sequencing technology through RNA Sequencing can identify candidate genes and potential SNPs quickly, thoroughly and comprehensively, as biomarkers for increasing both productivity (egg production, growth rate, and resistant to diseases) and meat quality (tenderness, flavor, meat fiber and fatty acid composition). During the last 6 years (2012-2018), several studies have been conducted on genes related to various trais: (1) disease resistance: toll receptor-4 (TLR4), mycovirus-1 (Mx-1), natural resistance associated macrophage-1 (NRAMP-1), inducible nitric oxide synthase (iNOS), transforming growth factor-β (TGF-β) genes; (2) meat production: growth hormone receptor (GH-r), growth hormone secretagogue receptor (GHSR) genes; (3) meat quality: calpastatine (CAST), calpain (CAPN) and myostatin (MSTN) genes; and (4) composition of fatty acids: stearyol CoA desaturase (SCD) and salute carrier (SLC) genes. Genetic quality of native and local chickens might be improved to increase their production and meat quality in order to build the Indonesian chicken industry.

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RNA deep sequencing reveals novel transcripts and pathways involved in the unsaturated fatty acid metabolism in chicken

Cited by 4 publications

References 50 publications

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep

Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken

The genetic quality improvement of native and local chickens to increase production and meat quality in order to build the Indonesian chicken industry

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