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. 2022 Jun 16:9:892024.
doi: 10.3389/fvets.2022.892024. eCollection 2022.

RNA Sequencing of the Pituitary Gland and Association Analyses Reveal PRKG2 as a Candidate Gene for Growth and Carcass Traits in Chinese Ningdu Yellow Chickens

Xinwei Xiong  1   2 , Min Zhou  1   2 , Xuenong Zhu  1   2 , Yuwen Tan  1   2 , Zhangfeng Wang  1   2 , Jishang Gong  1   2 , Jiguo Xu  1   2 , Yafang Wen  1   2 , Jianxiang Liu  1   2 , Xutang Tu  1   2 , Yousheng Rao  1   2
Affiliations

RNA Sequencing of the Pituitary Gland and Association Analyses Reveal PRKG2 as a Candidate Gene for Growth and Carcass Traits in Chinese Ningdu Yellow Chickens

Xinwei Xiong et al. Front Vet Sci. .

Abstract

Growth and carcass traits are of great economic importance to the chicken industry. The candidate genes and mutations associated with growth and carcass traits can be utilized to improve chicken growth. Therefore, the identification of these genes and mutations is greatly importance. In this study, a total of 17 traits related to growth and carcass were measured in 399 Chinese Ningdu yellow chickens. RNA sequencing (RNA-seq) was performed to detect candidate genes using 12 pituitary gland samples (six per group), which exhibited extreme growth and carcass phenotypes: either a high live weight and carcass weight (H group) or a low live weight and carcass weight (L group). A differential expression analysis, utilizing RNA-seq, between the H and L groups identified 428 differentially expressed genes (DEGs), including 110 up-regulated genes and 318 down-regulated genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the identified genes showed a significant enrichment of 158 GO terms and two KEGG pathways, including response to stimulus and neuroactive ligand-receptor interaction, respectively. Furthermore, RNA-seq data, qRT-PCR, and quantitative trait transcript (QTT) analysis results suggest that the PRKG2 gene is an important candidate gene for growth and carcass traits of Chinese Ningdu yellow chickens. More specifically, association analyses of a single nucleotide polymorphism (SNP) in PRKG2 and growth and carcass traits showed that the SNP rs16400745 was significantly associated with 12 growth and carcass traits (P < 0.05), such as carcass weight (P = 9.68E-06), eviscerated weight (P = 3.04E-05), and semi-eviscerated weight (P = 2.14E-04). Collectively, these results provide novel insights into the genetic basis of growth in Chinese Ningdu yellow chickens and the SNP rs16400745 reported here could be incorporated into the selection programs involving this breed.

Keywords: Ningdu yellow chickens; PRKG2 gene; RNA-seq; candidate gene; growth and carcass traits.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Correlation analysis among 17 traits related to growth and carcass.
Figure 2
Figure 2
The changes in whole gene transcripts between the H and L groups. PLS-DA plot of whole gene transcripts indicating the significant differentiation of gene expression profiles between the H and L groups.
Figure 3
Figure 3
Representation of the differentially expressed genes between the H and L groups. The x-axis values are the log2 (fold change) and the y-axis values are –log10 FDR. Genes with higher expression levels in H group compared with L group were denoted as “up-regulated” and indicated in red, while those with lower expression levels in H group were “down-regulated” and indicated in blue.
Figure 4
Figure 4
Functional annotation of DEGs by gene ontology (GO) analysis. The bar plot represents the gene counts within each GO category. All function or process terms listed have enrichment of FDR <0.05. (A) Biological process (top 10). (B) Cellular component (top 10). (C) Molecular function.
Figure 5
Figure 5
Differential expression levels of the following DEGs between H and L groups was confirmed by qRT–PCR. The x-axis indicates the DEGs, and the y-axis shows the relative quantity (RQ) value. The P value of each pair of comparison is presented in the figure. *P < 0.05; **P < 0.01; ***P < 0.001. H group: gray bars; L group: white bars.
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