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

Sahoo, Lakshman; Patel, A.K.; Sahu, Basanta Pravas; Meher, Prem Kumar; Mahapatra, Kanta Das; Dash, Sanjaya K.; Jayasankar, P.; Das, Paramananda

doi:10.1007/s12041-015-0528-7

Cited by 14 publications

(10 citation statements)

References 65 publications

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“…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.…”

Section: Introductionmentioning

confidence: 70%

“…Further, the Illumina PE reads were mapped to assembly sequences for analyzing depth distribution for every base in the genome. The accuracy of the assembly was evaluated by anchoring the scaffolds onto published SNP and microsatellite marker maps for rohu (Robinson et al, 2014;Sahoo et al, 2015). For this, SNPs and microsatellite markers of rohu were used as queries against rohu scaffolds by Blastn module as implemented in the program CLC Bio workbench version 7.0.4, with the following parameters: e-value 1e-10, word size 10, match 2, mismatch −3 and % identity 90%.…”

Section: De Novo Genome Assembly and Validationmentioning

confidence: 99%

“…We assessed the accuracy of the assembly by anchoring sequences onto the SNP and SSR-based genetic maps of rohu (Robinson et al, 2014;Sahoo et al, 2015). All SNP markers (3,193) with the sequence information matched at unique positions in 667 scaffolds, covering approximately 80% of the genome (Supplementary Table 3).…”

Section: Genome Assembly and Validationmentioning

confidence: 99%

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

et al. 2020

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Section: Introductionmentioning

confidence: 70%

Section: De Novo Genome Assembly and Validationmentioning

confidence: 99%

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

et al. 2020

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“…Maximum number of bases interrupting between two SSRs in a compound microsatellite was taken as 100. For the analysis of microsatellite polymorphism, DNA from 3 parents belonging to two linkage mapping panels of rohu [ 33 ] and 2 individuals (one each) from resistant and susceptible lines of rohu against aeromoniasis [ 5 ] was used to test the gene loci for diversity. Number of alleles, observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) were estimated using CERVUS software ver 3.0 ( http://www.fieldgenetics.com/pages/home.jsp ).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2015

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Rohu is a leading candidate species for freshwater aquaculture in South-East Asia. Unlike common carp the monsoon breeding habit of rohu restricts its seed production beyond season indicating strong genetic control over spawning. Genetic information is limited in this regard. The problem is exacerbated by the lack of genomic-resources. We identified 182 reproduction-related genes previously by Sanger-sequencing which were less to address the issue of seasonal spawning behaviour of this important carp. Therefore, the present work was taken up to generate transcriptome profile by mRNAseq. 16GB, 72bp paired end (PE) data was generated from the pooled-RNA of twelve-tissues from pre-spawning rohu using IlluminaGA-II-platform. There were 64.97 million high-quality reads producing 62,283 contigs and 88,612 numbers of transcripts using velvet and oases programs, respectively. Gene ontology annotation identified 940 reproduction-related genes consisting of 184 mainly associated with reproduction, 223 related to hormone-activity and receptor-binding, 178 receptor-activity and 355 embryonic-development related-proteins. The important reproduction-relevant pathways found in KEGG analysis were GnRH-signaling, oocyte-meiosis, steroid-biosynthesis, steroid-hormone biosynthesis, progesterone-mediated oocyte-maturation, retinol-metabolism, neuroactive-ligand-receptor interaction, neurotrophin-signaling and photo-transduction. Twenty nine simple sequence repeat containing sequences were also found out of which 12 repeat loci were polymorphic with mean expected-&-observed heterozygosity of 0.471 and 0.983 respectively. Quantitative RT-PCR analyses of 13-known and 6-unknown transcripts revealed differences in expression level between preparatory and post-spawning phase. These transcriptomic sequences have significantly increased the genetic-&-genomic resources for reproduction-research in Labeo rohita.

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“…Certain attributes like high allelic diversity, codominant inheritance, high abundance and genomewide distribution have made microsatellite markers a versatile genetic marker system. In our previous studies, 554 SSR markers were developed, the first generation linkage map constructed for L. rohita (Das et al 2005;Patel et al 2009;Sahoo et al 2015), and were extensively tested for cross-species transferability in Labeo bata (Patel et al 2010). Preliminary studies of microsatellite marker-based parentage assignment on rohu resulted in poor matching rates (Meher et al 2014).…”

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confidence: 99%

A molecular tool for parentage analysis in Indian major carp, Labeo rohita (Hamilton, 1822)

et al. 2016

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Determination of genealogical relationship between broodstock and progeny is important to estimate selection response in aquaculture breeding programs. Currently, the application of microsatellite markers for parentage determination is gaining popularity in aquaculture. In the present study, 17 simple sequence repeat markers were evaluated for parentage assignment on rohu. The allele frequencies, exclusion probabilities and polymorphic information contents (PIC) were calculated using Cervus. The polymorphic information content values showed that most of the microsatellite markers were highly informative (PIC > 0.7). Based on the exclusion power, eight microsatellite markers were chosen for parentage assignment. The robustness of this suite was assessed in five full-sib and four halfsib families using two contrasting methods, a pair-wise likelihood comparison approach in Cervus and a full-pedigree likelihood method in the COLONY program. Using real data set, the correct matching rate was more than 98%, comparable to the simulated study (99.9%) in the case of Cervus 3.0 and 100% in the case of COLONY. The result of the present study implies that this set of microsatellites would be an effective tool for parentage and sibship identification, testing performance of families and estimating genetic parameters in the ongoing selective breeding program of rohu.

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

Cited by 14 publications

References 65 publications

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

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

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

A molecular tool for parentage analysis in Indian major carp, Labeo rohita (Hamilton, 1822)

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