Genome-wide discovery and in silico mapping of gene-associated SNPs in Nile tilapia

Xia, Jun; Wan, Zi Yi; Ng, Zhen Long; Wang, Le; Fu, Gui Hong; Lin, Grace; Liu, Feng; Yue, Gen Hua

doi:10.1016/j.aquaculture.2014.04.028

Cited by 39 publications

(29 citation statements)

References 51 publications

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“…Therefore, only a small set of SNPs covering the whole genome would be required to conduct genome-wide association studies (GWAS) for important traits for marker-assisted selection (MAS). By using the published linkage maps 12 and in-silico mapping, 42 over 10,000 detected SNPs (Supplementary Fig. S1, Supplementary Materials) were mapped to 16 linkage groups, supplying a useful resource for quantitative trait loci (QTL) mapping and GWAS for traits.…”

Section: Resultsmentioning

confidence: 99%

Draft genome sequence of an eliteDurapalm and whole-genome patterns of DNA variation in oil palm

Jin

Lee

Bai

et al. 2016

DNA Res

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Oil palm is the world’s leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits.

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Section: Resultsmentioning

confidence: 99%

Draft genome sequence of an eliteDurapalm and whole-genome patterns of DNA variation in oil palm

Jin

Lee

Bai

et al. 2016

DNA Res

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“…The weight of tilapia fillet contributes heavily towards the yield per fish, which is an important parameter in the aquaculture industry1828. Here, we report the first methylome of skeletal muscle tissue, including sexually dimorphic DMRs, in hybrid tilapia, which is genetically close to Nile tilapia2122. We discovered that MAPK/ERK signaling pathway overexpression in male tilapia was associated with superior growth rate in male tilapia.…”

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confidence: 90%

“…The superior growth rate of male tilapias has driven large sectors of the tilapia aquaculture industry to develop all-male tilapia populations for production using sex-reversal techniques18. In addition, the genome sequence of a Nile tilapia has been sequenced19, and other genomic resources, including microsatellites20, genome-wide SNPs2122, linkage maps232425 and QTL for important traits2526, are available. Hence, tilapia is a good model for studying the molecular mechanisms underlying SD.…”

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confidence: 99%

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

Wan

Xia

Lin

et al. 2016

Sci Rep

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Sexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination. CpG methylation in promoter regions was negatively correlated with the gene expression level. MAPK/ERK pathway was upregulated in male tilapia. We also inferred active cis-regulatory regions (ACRs) in skeletal muscle tissues from WGBS datasets, revealing sexually dimorphic cis-regulatory regions. These results suggest that DNA methylation contribute to sex-specific phenotypes and serve as resources for further investigation to analyze the functions of these regions and their contributions towards sexual dimorphisms.

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“…Despite the ongoing efforts to increase the growth performance of hybrid salt tolerant tilapias for culture, there has been mixed results due to the vague genetic background of the parental strains [21]. Fortunately, an increasing number of genomic resources are publicly available for tilapia, such as microsatellites [22], single nucleotide polymorphisms (SNPs) [23,24], genetic and physical maps [25,26,27,28], expressed sequence tags (ESTs) [29], whole genome assembly [30] as well as QTL for economical traits [4,31,32]. These resources provide the essential tools in MAS of tilapia.…”

Section: Introductionmentioning

confidence: 99%

Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus)

et al. 2016

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In aquaculture, growth and sex are economically important traits. To accelerate genetic improvement in increasing growth in salt-tolerant tilapia, we conducted QTL mapping for growth traits and sex with an F2 family, including 522 offspring and two parents. We used 144 polymorphic microsatellites evenly covering the genome of tilapia to genotype the family. QTL analyses were carried out using interval mapping for all individuals, males and females in the family, respectively. Using all individuals, three suggestive QTL for body weight, body length and body thickness respectively were detected in LG20, LG22 and LG12 and explained 2.4% to 3.1% of phenotypic variance (PV). When considering only males, five QTL for body weight were detected on five LGs, and explained 4.1 to 6.3% of PV. Using only females from the F2 family, three QTL for body weight were detected on LG1, LG6 and LG8, and explained 7.9–14.3% of PV. The QTL for body weight in males and females were located in different LGs, suggesting that in salt-tolerant tilapia, different set of genes ‘switches’ control the growth in males and females. QTL for sex were mapped on LG1 and LG22, indicating multigene sex determination in the salt-tolerant tilapia. This study provides new insights on the locations and effects of QTL for growth traits and sex, and sets the foundation for fine mapping for future marker-assisted selection for growth and sex in salt-tolerant tilapia aquaculture.

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Genome-wide discovery and in silico mapping of gene-associated SNPs in Nile tilapia

Cited by 39 publications

References 51 publications

Draft genome sequence of an eliteDurapalm and whole-genome patterns of DNA variation in oil palm

Draft genome sequence of an eliteDurapalm and whole-genome patterns of DNA variation in oil palm

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus)

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