Identification of reproduction-related genes and SSR-markers through expressed sequence tags analysis of a monsoon breeding carp rohu, Labeo rohita (Hamilton)

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

“…A 17% higher average growth rate per generation was achieved after four generations of selection (Das Mahapatra et al, 2006). Our previous studies have also reported DNA markers such as SSRs (Das et al, 2005;Patel et al, 2009;Sahu et al, 2012), SSR and SNP -based linkage maps (Robinson et al, 2014;Sahoo et al, 2015) and transcriptome resources (Robinson et al, 2012;Sahu et al, 2013) in this species. However, whole genome sequence of rohu carp is still lacking.…”

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)

“…The Indian major carp Labeo rohita (Hamilton), a cyprinid is a leading candidate species for freshwater aquaculture not only in India but also in the whole sub-continent of South-East Asia with the annual production of 1.5 million tonnes in 2012 [ 1 ]. Due to its immense economic, ecological and cultural importance it received lot of research interest in different areas including culture [ 2 ], breeding [ 3 ] immunology [ 4 ], disease ecology [ 5 ], reproductive physiology [ 6 ] and nutrition [ 7 ]. One of the major problem in this species is highly monsoon dependent breeding habit [ 8 ] and inability to breed in confined pond water without hormonal induction [ 9 ].…”

“…Addressing issues like gonad maturation; spawning and seed production under changing climatic conditions will require comprehensive information on a number of reproduction-related genes. In our earlier attempt 182 reproduction-related genes were identified from 4,642 high-quality ESTs by Sanger sequencing [ 6 ], but the number was less. High throughput next generation sequencing technologies provide the platforms to generate transcriptome sequences with much lower cost than traditional Sanger method, thus the transcripts generated by NGS technology can boost genetic and genomic research of relatively lagging species [ 19 ].…”

“…SSRs derived from expressed sequence tags (ESTs) have special advantages such as those might be linked to known genes, having higher transferability among related species, lower cost for development and higher proportion of high-quality markers [ 20 ]. Transcriptome resources for reproductive tissues are currently available for other commercially important fishes, including channel catfish ( Ictalurus punctatus ) [ 21 ], common carp ( Cyprinus carpio ) [ 19 ], zebrafish ( Danio rerio ) [ 22 ], rainbow trout ( Oncorhynchus mykiss ) [ 23 , 24 ], coho salmon ( Oncorhynchus kisutch ) [ 25 ], tilapia ( Oreochromis mossambicus ) [ 26 ], Atlantic halibut ( Hippoglossus hippoglossus ) [ 27 ], senegalese sole ( Solea senegalensis ) [ 28 ], Atlantic salmon ( Salmo salar ) [ 29 ], and cod ( Gadus morhua ) [ 30 ] but less information is available for L rohita [ 5 , 6 ].…”

Preliminary genetic linkage map of Indian major carp, Labeo rohita (Hamilton 1822) based on microsatellite markers

“…Integration of modern molecular biological tools, along with conventional breeding programmes, provides speed, reliability and sustainability in producing improved varieties. An ongoing selective breeding programme in rohu, which started in 1992 at Central Institute of Freshwater Aquaculture, has achieved 17% higher growth per generation (Mahapatra et al 2007), whereas markers needed to achieve further accelerated genetic improvement in rohu have just begun (Patel et al 2009;Robinson et al 2012;Sahu et al 2013). The outcome of such an effort is the generation of a genetic linkage map, based on SNP derived from transcribed sequences (Robinson et al 2014).…”