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Research Article Transcriptome Analysis Reveals the Genes Involved in Growth and Metabolism in Muscovy Ducks

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Research Article Transcriptome Analysis Reveals the Genes Involved in Growth and Metabolism in Muscovy Ducks Hindawi BioMed Research International Volume 2021, Article ID 6648435, 9 pages https://doi.org/10.1155/2021/6648435 Research Article Transcriptome Analysis Reveals the Genes Involved in Growth and Metabolism in Muscovy Ducks Xingxin Wang ,1,2 Yingping Xiao ,2 Hua Yang ,2 Lizhi Lu,3 Xiuting Liu,2 and Wentao Lyu 2 1College of Animal Science, ZheJiang A&F University, Hangzhou, China 2State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China 3Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China Correspondence should be addressed to Wentao Lyu; [email protected] Received 28 October 2020; Revised 31 March 2021; Accepted 9 April 2021; Published 19 April 2021 Academic Editor: Yong Feng Copyright © 2021 Xingxin Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Muscovy ducks are among the best meat ducks in the world. The objective of this study was to identify genes related to growth metabolism through transcriptome analysis of the ileal tissue of Muscovy ducks. Duck ileum samples with the highest (H group, n =5) and lowest (L group, n =5) body weight were selected from two hundred 70-day-old Muscovy ducks for transcriptome analysis by RNA sequencing. In the screening of differentially expressed genes (DEGs) between the H and L groups, a total of 602 DEGs with a fold change no less than 2 were identified, among which 285 were upregulated and 317 were downregulated. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that glutathione metabolism, pyrimidine metabolism, and protein digestion and absorption processes played a vital role in regulating growth and metabolism. The results showed that 7 genes related to growth and metabolism, namely, ANPEP, ENPEP, UPP1, SLC2A2, SLC6A19, NME4, and LOC106034733, were significantly expressed in group H, which was consistent with the phenotype results. The validation of these 7 genes using real-time quantitative PCR results indicated that the expression level of ENPEP was significantly different between the H and L groups (P <0:05). This study provides a theoretical basis for exploring the influence of the ileum on growth and metabolism in ducks. 1. Introduction broilers. Changing the structure of the intestinal flora is another way to modulate the growth and metabolism pro- Duck meat is one of the most important meat sources in Asia cess. Many studies have shown that regulating the structure with a high content of essential unsaturated fatty acids and is of the intestinal flora can indeed affect the growth of animals. healthier than pork. It is popular in China and Southeast Dietary supplementation with Lactobacillus acidophilus can Asian countries. Native to the tropical regions of South and change the structure of the intestinal microflora and thus Central America, Muscovy ducks (Cairina moschata)have increase body weight gain in Ross broiler chickens [3]. been gradually domesticated since their introduction into Lactobacillus fed to poultry reduces colonization by human China. Because of their good meat quality, low adipose tissue foodborne pathogens such as Campylobacter, Clostridium content, high lean meat rate, and high protein content [1], difficile, and Salmonella in the gastrointestinal tract and pro- Muscovy ducks have become an excellent meat duck in China. motes the growth of poultry [4]. The first two methods lead At present, there are two ways to regulate the growth and to changes in gene expression, which is the fundamental rea- metabolism of poultry. The first is to change the nutrient son why they can regulate the growth and metabolism of level in the diet. Gonzalez-Esquerra and Leeson [2] showed poultry. Food intake, energy expenditure, and energy balance that high-protein diets increased daily body weight gain in are regulated by cellular and molecular mechanisms. For 2 BioMed Research International example, a methionine deficient diet decreasing the body RNA Purification Kit (Invitrogen, USA), and treated with a weight gain and increasing feed conversion ration might RNase-Free DNase Set (Qiagen, USA) according to the be due to the gene expression alteration of amino acid manufacturer’s instructions. RNA purity was monitored by transporters in different tissues of chickens, such as a NanoPhotometer® spectrophotometer (IMPLEN, USA) Sodium-coupled Neutral Amino Acid Transporter (SNAT1), using OD260/280 and OD260/230 ratios. The quantity of Aromatic Amino Acid Transporter (TAT1), and so on RNA was determined by a NanoDrop spectrophotometer (Fagundes et al., 2020). (Thermo Fisher Scientific Inc., USA). The integrity and con- Transcriptome sequencing, also known as RNA sequenc- tamination of RNA samples were checked by 1% agarose gel ing (RNA-seq), is a technique used to explore and quantita- electrophoresis. The integrity of RNA samples was evaluated tively describe the differences in gene types and expression using the RNA Nano 6000 Assay Kit of the Agilent Bioanaly- levels at a global level [5]. It could also intuitively link zer 2100 system (Agilent Technologies, USA). changes at the gene level with phenotypic changes. With fi the development of this technique, livestock genetics and 2.3. Library Construction and Sequencing. The quali ed RNA breeding have been greatly improved. The genetic mecha- samples with the RIN (Supplementary Table 1) no less than 6 nism affecting traits can be studied at the molecular level to were used to construct cDNA sequencing libraries of the ileal select candidate genes, which will be helpful for breeding transcriptome of Muscovy ducks using the NEBNext® ™ improvement in Muscovy ducks. Wang et al. used RNA-seq Ultra RNA Library Prep Kit for Illumina® (NEB, USA) ’ to analyze the caecum of chickens in an E. tenella infection following the manufacturer s recommendations. After cluster group and an uninfected group and found that the generation by the cBot Cluster Generation System using a ANGPTL4, MAPK10, and CD44 genes played an important TruSeq PE Cluster Kit v3-cBot-HS (Illumina), the libraries role in the invasion of E. tenella []. Chen et al. conducted were sequenced on an Illumina HiSeq 6000 platform for the transcriptome analysis on the breast muscles of fast- and generation of 150 bp paired-end reads. slow-growing chickens and revealed that the SNCG, PLPPR4, 2.4. Data Processing and Transcriptome Assembly. Raw reads and VAMP1 genes were related to growth and metabolism in were first processed through in-house Perl scripts to obtain Jinghai yellow chickens [7]. clean reads by removing reads containing adapters, reads The energy used for growth and metabolism in animals is containing poly-N sequences, and low-quality reads. These mainly obtained from the digestion of nutrients in the small reads were used for the de novo assembly using Trinity [8] intestine. As the third portion of the small intestine, the software. The outputs of Trinity are sequences called uni- ileum functions to absorb nutrients from foods and transfer genes that can form either clusters in which the similarity them into the bloodstream of the body to provide energy among sequences is >70% or unigenes that are unique and and essential nutrients to the host. Consequently, genes form the singletons [9]. The transcriptional sequences expressed in the ileum are key to modulating the growth obtained by Trinity splicing were used as the reference and metabolism of animals. To date, few studies have identi- genome (Ref) for subsequent analysis. Clean reads of each fied the key genes involved in regulating the growth and sample were mapped on the Ref to filter out the reads with development of ducks. The intestine is essential for absorbing a comparison quality value lower than 10, the reads on the nutrients in the body. This study analyzed the ileal tran- unpaired comparison, and the reads in multiple regions of scriptome of Muscovy ducks to identify the genes related to the genome in order to get mapping reads for each sample. growth and metabolism. By doing so, it provides a theoretical The raw transcriptome read data are available in the SRA basis for the genetic regulation of duck growth and database under accession number PRJNA669499. metabolism. 2.5. Differential Gene Expression Analysis. Differential 2. Materials and Methods expression analysis of the H and L groups was performed using the DESeq R package (1.10.1). DESeq provides statisti- 2.1. Animals and Sampling. The animal processes in this cal routines for determining differential expression in digital study were approved by the Animal Care Committee of gene expression data using a model based on the negative bino- Zhejiang Academy of Agriculture Sciences (ZAASDLSY2019- mial distribution. The resulting P values were adjusted using 1910). All the ducks were obtained from Hewang Poultry Benjamini and Hochberg’sapproachforcontrollingthefalse Industry Co., Ltd. (Lanxi, China). A total of 200 healthy Mus- discovery rate. Genes with an adjusted P value < 0.05 found covy ducks, which were randomly selected from a population by DESeq were assigned as differentially expressed. of 5000 70-day-old ducks, were weighed individually. Among these 200 ducks, the 5 ducks with the highest body weight 2.6. GO and KEGG Enrichment Analysis of Differentially and 5 ducks with the lowest body weight were set as the H Expressed Genes. Gene Ontology (referred to as GO, http:// group and the L group, respectively. After the ducks were www.geneontology.org/) enrichment analysis of the differen- slaughtered, the ileum segments were collected, immediately tially expressed genes (DEGs) was implemented by the frozen in liquid nitrogen, and then stored at -80°CuntilRNA GOseq R package-based Wallenius noncentral hypergeo- isolation. metric distribution [10], which can adjust for gene length bias in DEGs.
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