A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish

Geng, Xin; Liu, Shikai; Yao, Jun; Bao, Lisui; Zhang, Jiaren; Li, Chao; Wang, Ruijia; Jiang, Sha; Zeng, Peng; Zhi, Degui; Liu, Zhanjiang

doi:10.1534/g3.116.032201

Cited by 60 publications

(34 citation statements)

References 71 publications

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“…Recently, we developed the catfish 250 K SNP array using Affymetrix axiom technology30. This array has been of great use for various genetic analysis including genetic linkage mapping2628 and analysis of performance traits using GWAS313233. However, the 250 K SNP array was designed without a reference genome.…”

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Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Zeng

et al. 2017

Sci Rep

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Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence. Here we also report linkage mapping using the 690 K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. These markers were mapped to 29 linkage groups (LGs) with 30,591 unique marker positions. This linkage map anchored 1,602 scaffolds of the reference genome sequence to LGs, accounting for over 97% of the total genome assembly. A total of 1,007 previously unmapped scaffolds were placed to LGs, allowing validation and in few instances correction of the reference genome sequence assembly. This linkage map should serve as a valuable resource for various genetic and genomic analyses, especially for GWAS and QTL mapping for genes associated with economically important traits.

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Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Zeng

et al. 2017

Sci Rep

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“…The expression pattern of myh14 in zebrafish revealed its species-specific functions in fish muscle formation 64 , implying that this gene may influence the swimming ability of fish. The candidate gene rgs9bp is a regulator of G-protein signaling, which involves in bone metabolism in catfish 65 . Whereas, cldn10a and cldn10b are associated with salinity regulation in Japanese medaka ( Oryzias latipes ) 66 .…”

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confidence: 99%

Quantitative trait loci mapping for feed conversion efficiency in crucian carp (Carassius auratus)

Pang

et al. 2017

Sci Rep

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QTL is a chromosomal region including single gene or gene clusters that determine a quantitative trait. While feed efficiency is highly important in aquaculture fish, little genetic and genomic progresses have been made for this trait. In this study, we constructed a high-resolution genetic linkage map in a full-sib F1 family of crucian carp (Carassius auratus) consisting of 113 progenies with 8,460 SNP markers assigning onto 50 linkage groups (LGs). This genetic map spanned 4,047.824 cM (0.478 cM/marker) and covered 98.76% of the crucian carp genome. 35 chromosome-wide QTL affecting feed conversion efficiency (FCE, 8 QTL), relative growth rate (RGR, 9 QTL), average daily gain (ADG, 13 QTL) and average daily feed intake (ADFI, 5 QTL) were detected on 14 LGs, explaining 14.0–20.9% of the phenotypic variations. In LGs of LG16, LG25, LG36 and LG49, several QTL affecting different traits clustered together at the identical or close regions of the same linkage group. Seven candidate genes, whose biological functions may involve in the energy metabolism, digestion, biosynthesis and signal transduction, were identified from these QTL intervals by comparative genomics analysis. These results provide a basis for elucidating genetic mechanism of feed efficiency and potential marker-assisted selection in crucian carp.

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“…This method captures the linkage disequilibrium (LD) between markers and causative mutations that tend to be inherited together across generations [21]. GWAS has been applied to provide insights into both the genetic architecture and loci underpinning the genetic variation of growth-related traits in different aquaculture species, including Atlantic salmon and catfish [22][23][24][25], using high-density SNPs arrays (ranging from 108 K to 218 K SNPs) and, more recently, Nile tilapia by using a medium-density (50 K) SNP array [19].…”

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Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Yoshida¹,

Yáñez²

2020

Preprint

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Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromos niloticus) using genotypes imputed to whole-genome sequence (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1,309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13% to 44%, depending on the trait analyzed. The better resolution of the WGS data combined with the increased power of the mtGWAS approach, allowed the detection of significant markers not previously found in the stGWAS. Some lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions: The high-resolution mtGWAS presented, allowed identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

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A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish

Cited by 60 publications

References 71 publications

Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

Quantitative trait loci mapping for feed conversion efficiency in crucian carp (Carassius auratus)

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

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