Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production

Egg production is an important economic trait and a key indicator of reproductive performance in ducks. Egg production is regulated by several factors including genes. However the genes involved in egg production in duck remain unclear. In this study, we compared the ovarian transcriptome of high egg laying (HEL) and low egg laying (LEL) ducks using RNA-Seq to identify the genes involved in egg production. The HEL ducks laid on average 433 eggs while the LEL ducks laid 221 eggs over 93 weeks. A total of 489 genes were found to be significantly differentially expressed out of which 310 and 179 genes were up and downregulated, respectively, in the HEL group. Thirty-eight differentially expressed genes (DEGs), including LHX9, GRIA1, DBH, SYCP2L, HSD17B2, PAR6, CAPRIN2, STC2, and RAB27B were found to be potentially related to egg production and folliculogenesis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that DEGs were enriched for functions related to glutamate receptor activity, serine-type endopeptidase activity, immune function, progesterone mediated oocyte maturation and MAPK signaling. Protein–protein interaction network analysis (PPI) showed strong interaction between 32 DEGs in two distinct clusters. Together, these findings suggest a mix of genetic and immunological factors affect egg production, and highlights candidate genes and pathways, that provides an understanding of the molecular mechanisms regulating egg production in ducks and in birds more broadly.