Abstract
BackgroundCarp 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.ResultA 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.ConclusionThis 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.
Highlights
Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm
Molecular mediation of reproductive seasonality and key candidate genes We report a total of 137 key candidate genes controlling reproductive seasonality and its major pathways operating in four tissues, viz., brain, pituitary, gonad and liver
Genes expressed in liver associated with innate immune system can be used for biomonitoring of fish mortality [77]. This is the first report in carp fish rohu deciphering candidate genes of circannual biological rhythm of reproduction along with biological clock genes (BCGs)
Summary
Rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. 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. Though prolific breeder like common carp and zebra fish breed independent of season but vast majority of the freshwater fishes of Indian subcontinent breed seasonally during the monsoon season (June–August) when rainfall is heaviest [1] This rhythm reflects evolution of differential biological clock. In order to decipher candidate genes regulating seasonal fish breeding, RNA sequencing of associated tissues are imperative Such data can be used to construct gene regulatory networks (GRNs) to depict process of cell differentiation, metabolism, cell cycle and signal transduction in the biological system. Understanding dynamics of these networks can shed light on mechanism of reproductive seasonality
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