Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Abstract

Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. Result A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. Conclusion This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita

“…As we had to identify genes linked to high body weight concurrent with high EBV, we selected six fish/groups, i.e., LB and HB, based on earlier reports ( Danzmann et al, 2016 ; Lin et al, 2019 ; Shen et al, 2022 ). Clean and trimmed reads generated had GC content ranging from 37% to 42%, which is similar to previous reports ( Das et al, 2020 ; Jaiswal et al, 2021 ). BUSCO analysis indicated that our transcriptome had partial to complete gene information for 86.31% of the genes when compared with the eukaryote orthologous set.…”

Analysis of reproduction-related transcriptomes on pineal-hypothalamic-pituitary-ovarian tissues during estrus and anestrus in Tan sheep

“…It has been found that animal reproduction activity varies with the seasons, which is not only related to the ambient temperature and light, but also closely related to the endogenous regulation of animals themselves. Studies have shown that genes involved in the regulation of animal reproduction change rhythmically with the seasons and play an important role in the regulation of seasonal reproduction ( 1 ). The reproductive activity of seasonal breeding animals is governed by a regulatory network of the Pineal—Hypothalamus—Pituitary—Ovary (PHPO) axis.…”