Open AccessTranscriptome analysis and identification of genes and single‐nucleotide polymorphisms associated with growth traits in the Chinese soft‐shelled turtle, Pelodiscus sinensis
Author(s) -
Zeng Dan,
Xiong Gang,
Wang Xiaoqing,
Zhou Xianwen,
Wang Pei,
Peng Na,
Luo Zhijia,
Li Xiao
Publication year - 2021
Publication title -
journal of the world aquaculture society
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.655
H-Index - 60
eISSN - 1749-7345
pISSN - 0893-8849
DOI - 10.1111/jwas.12780
Subject(s) - biology , transcriptome , gene , kegg , genetics , turtle (robot) , phenotype , single nucleotide polymorphism , candidate gene , gene expression , genotype , ecology
Abstract The Chinese soft‐shelled turtle, Pelodiscus sinensis , is an important aquaculture species in China. Understanding the molecular mechanisms of growth regulation may contribute to its genetic improvement and lead to increases in the production. Growth rate in this species varies greatly among individuals, and the variation apparently has a genetic basis. To identify growth‐related genes and explore the molecular mechanism of its growth regulation, fast‐growing and slow‐growing turtles were selected from two growth stages, juveniles or adults, respectively, for transcriptome sequencing with liver tissue using the Illumina sequencing platform. Analyses showed that, in juveniles, 303 genes were differentially expressed, of which 217 genes were expressed at higher levels in the fast‐growing turtles. In adults, 1,093 genes were differentially expressed, of which 682 genes were expressed at higher levels in the fast‐growing turtles. Gene Ontology (GO) enrichment of differentially expressed genes (DEGs) identifies three functional groups being significantly enriched in juveniles, but 71 functional groups in adults. Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs in juveniles identified only one pathway being significantly enriched, the proxisome proliferator‐activated receptor (PPAR) signaling pathway, while eight pathways mostly related to fatty acid metabolism were identified in adults. These findings suggest that regulation of growth is more complicated and involves more genes and pathways in adults compared with juveniles, and metabolic or metabolic‐related genes may relate to the growth difference of P. sinensis . Some key genes related to growth were identified from another six growth‐related signaling pathways, and DEGs in GH‐IGF 1 axis genes and Jak–STAT signaling pathway might play important roles in the growth difference of P. sinensis . In addition, 73 single‐nucleotide polymorphisms (SNPs) from 23 growth‐related genes were successfully genotyped. Growth association analysis in 280 individuals revealed that 2 SNPs in 2 key genes ( IGF2R and SLC27A2 ) were associated with growth of P. sinensis . This study provides information on key genes, SNPs, and biological processes that may be involved in growth and highlights the differentiation of growth regulation in different growth stages of P. sinensis .