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Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues.

ABSTRACT: While the chicken (Gallus gallus) is the most consumed agricultural animal worldwide, the chicken transcriptome remains understudied. We have characterized the transcriptome of 10 cell and tissue types from the chicken using RNA-seq, spanning intestinal tissues (ileum, jejunum, proximal cecum), immune cells (B cells, bursa, macrophages, monocytes, spleen T cells, thymus), and reproductive tissue (ovary). We detected 17,872 genes and 24,812 transcripts across all cell and tissue types, representing 73% and 63% of the current gene annotation, respectively. Further quantification of RNA transcript biotypes revealed protein-coding and lncRNAs specific to an individual cell/tissue type. Each cell/tissue type also has an average of around 1.2 isoforms per gene, however, they all have at least one gene with at least 11 isoforms. Differential expression analysis revealed a large number of differentially expressed genes between tissues of the same category (immune and intestinal). Many of these differentially expressed genes in immune cells were involved in cellular processes relating to differentiation and cell metabolism as well as basic functions of immune cells such as cell adhesion and signal transduction. The differential expressed genes of the different segments of the chicken intestine (jejunum, ileum, proximal cecum) correlated to the metabolic processes in nutrient digestion and absorption. These data should provide a valuable resource in understanding the chicken genome.

SUBMITTER: Overbey EG

PROVIDER: S-EPMC8278112 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:China has the richest local chicken breeding resources in the world and is the world's second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas. RESULTS:Eight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18?K SNPs were selected in the final array. It consists of: (i) 19.22?K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98?K SNPs related to economic traits from the Illumina 60?K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63?K SNPs from 861 candidate genes of economic traits; (iv) the 0.94?K SNPs related to residual feed intake; and (v) 18.41?K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40?K - 47?K SNPs were polymorphic (with minor allele frequency?>?0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array. CONCLUSIONS:We successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600?K and Illumina 60?K arrays, there were 21,41?K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds.

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Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues.

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